The U.S. Secret Service said Thursday that the agency - which is heading security for the visit of Pope Francis in September - has not ordered Philadelphia businesses to close and did not dictate that SEPTA limit rail service that weekend.

The agency instead stressed that Philadelphia would be "open for business" when the pope visits.

Meanwhile, South Jersey sources confirmed that the Benjamin Franklin Bridge will be closed, and some universities in the area outlined plans to shut down that weekend.

"The Secret Service has not directed any of the transit systems to limit stops due to security concerns," a release Thursday night said. "However, the projected volume of people in attendance and the management of that projected crowd will likely impact the transit system's ability to operate on their normal schedule and stops."

SEPTA has drastically cut back the number of open stations and hours that Regional Rail trains will operate Sept. 26 and 27, the Saturday and Sunday with the pope's appearances. To manage the expected throngs of riders, the agency has announced a lottery will be held Monday for the opportunity to purchase daily passes for the weekend from a total of 350,000. It is planning for about triple the ridership it gets on a typical Saturday or Sunday.

An earlier plan to directly sell the passes online failed within minutes because thousands of would-be buyers crashed the system.

Reports that nearly all of Center City will essentially be shut down to vehicle traffic have raised concerns and frustration about access and the impact on workers, businesses, hospitals, and universities.

As many as 1.5 million people are expected to pour into the city the Saturday that Francis arrives to highlight events following the World Meeting of Families. He will deliver a major address on immigration and religious freedom at Independence Hall and later appear on the Benjamin Franklin Parkway for a Festival of Families celebration.

The next day, the crowds are expected to return when the pope celebrates Mass on the Parkway.

The pope's visit was designated a National Special Security Event by Secretary of Homeland Security Jeh Johnson in November. That means the agency designs and implements the city's security plan.

Secret Service spokesman Robert Hoback said that planning was continuing and that he would not release details on street closures or security zones.

"All these entities are working together, so someone says, 'Hey, we might want to consider moving this here,' and that changes the perimeter, the magnetometers, and it has a domino effect," he said. "If you change one piece, it will change three or four things associated, but that's normal."

The release stressed that the Secret Service was working with businesses and residents in an "unprecedented way."

"The City of Philadelphia has repeatedly stated that it will be open for business during this event. In fact, the Secret Service has taken unprecedented steps to work with local area business owners to help facilitate keeping the businesses in Center City Philadelphia open," it said.

"For example, within just the past month, Secret Service agents have begun to meet personally with business owners, residents, and others whose buildings have been identified to be within the secure zone. As with all large-scale security events, specific details are still in progress. However, agents will continue to have an open dialogue with those within the secure perimeter."

Hoback said agents will not suggest whether a business stays open.

"We don't recommend a business stays open or closed," Hoback said. "That's up to them. As soon as the information is final and we know it's not going to change, we'll put it out. When I say three weeks, that's based on past experiences. If we get everything compiled and done in four, we'll send it out."

Ben Franklin Bridge

Two sources with knowledge of planning in New Jersey said the plan as of now was for the Ben Franklin Bridge to close to vehicular traffic for parts or all of the weekend. At some point, I-676, Morgan Boulevard, and possibly the Admiral Wilson Boulevard in South Jersey will also be closed to traffic.

At least 1,100 tour buses are slated to park in central Camden and on the Camden waterfront.

Bus passengers will walk to the Ben Franklin Bridge plaza for security clearance before being allowed to walk across the bridge.

One of the sources noted barricades to be used in security perimeters are in such high demand, they are no longer available anywhere in the Northeastern United States and will have to be shipped in.

Universities

The pope's visit has also prompted Philadelphia's major universities to close for logistical reasons - or consider closing for some of the festivities. Some have established special planning committees to prepare.

Drexel University announced to staff that it plans to cancel classes at its University City, Center City, and Queen Lane campuses beginning Friday, Sept. 25, through that Sunday. Personnel deemed "essential" will be working to keep some campus offices and services open to serve students and visitors, the school said.

"Even with excellent planning, the event may strain the city's infrastructure," James Herbert, interim provost and senior vice president of academic affairs, wrote to Drexel staff in early July.

"We will all need to be flexible in our work, school, and travel plans."

Temple University plans to cancel classes at its Center City campus on the Saturday, but no decision has been made about its main campus in North Philadelphia.

"We're still studying the issues like everyone else, looking for good, reliable information to make decisions," said spokesman Ray Betzner.

The University of Pennsylvania expects to make a decision this week about its plans for the papal visit, a spokesman said.

New York and D.C.

The pope's visits to New York and Washington have also been designated National Special Security Events. Philadelphia has the highest crowd estimates, according to reports, largely because of its two large-scale events on the Parkway.

In Washington, Francis will say a Mass in Spanish at the Catholic University of America for 25,000 people. The event is ticketed, but Jumbotrons will be placed throughout the city, similar to Philadelphia's plan.

Francis will also make an appearance at the White House and address a joint session of Congress. The Secret Service would not reveal security plans for Washington - its timeline is also three weeks before the visit. One agent did refer to the Obama inauguration in 2013, in which a huge swath of downtown was shut down to vehicular traffic.

In New York, the pope will say a Mass at St. Patrick's Cathedral, open to clergy only.

He will also attend a small ticketed service at the National September 11 Memorial and say a Mass at Madison Square Garden. The Mass at the Garden will also be ticketed, and most tickets will go to New York Archdiocese parishes to be distributed among parishioners.

A spokesman for the New York Police Department said the city tries to minimize the impact that visiting heads of state, such as Francis, have on traffic and pedestrian movements, but some changes are necessary.

"Waist-high" barriers will likely be used for security at the memorial and museum, where Francis will address a tickets-only audience starting at 11:30 a.m. The police spokesman said he did not know if the streets immediately adjacent to the Garden would be closed during the Mass, which starts at 6 p.m. - the heart of rush hour in Midtown.

"When he is in transit, there will be some frozen areas, some street closures," the spokesman said. "But for the most part, we are not going to restrict movements."

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Inquirer staff writers David O'Reilly and Susan Snyder contributed to this article.