The US Secret Service director resigned Wednesday, paying the price for a string of security lapses by the elite presidential protection branch, including one in which an armed intruder ran into the White House.

Julia Pierson stepped down a day after enduring a withering public grilling by lawmakers, who pronounced themselves baffled at failures by Secret Service agents, another of which saw an armed former felon get on an elevator with President Barack Obama.

Pierson had been brought into the agency as a new broom after the reputation of its sharp-suited agents took a hit from drinking and prostitution scandals.

But she leaves with the Secret Service facing searching questions from critics who have even warned the lives of the president and his family are not safe, due to several high-profile failures.

Pierson resigns under pressure

Bowing to rising political pressure, Pierson offered her resignation and it was accepted by Homeland Security Secretary Jeh Johnson.

Johnson appointed Joseph Clancy -- who formerly headed the presidential protection branch of the Secret Service as an interim replacement.

An independent panel will be named to probe a September 19 incident, which saw knife-carrying homeless US army veteran Omar Gonzalez allegedly jump the White House fence and run into the residence.

Gonzalez pleaded not guilty on Wednesday to three counts including unlawfully entering a restricted building or grounds with a deadly or dangerous weapon.

In another incident last month, an armed security contractor with a criminal record was allowed into an elevator with Obama when he visited the Centers for Disease Control and Prevention in Atlanta, Georgia.

In another eye-opening development, Obama spokesman Josh Earnest said Wednesday the presidency had only been made aware of the full circumstances of the Atlanta incident shortly before it appeared in a report on Tuesday.

Pierson's sullen performance before angry lawmakers on Tuesday did little to shield her agency.

"It's clear that our security plan was not properly executed," Pierson said of the September 19 intrusion.

"This is unacceptable and I take full responsibility. And I will make sure that it does not happen again."

Following the hearing, Pierson was besieged by calls for her departure by angry lawmakers, even as the White House said it still had confidence in her.

Leading Democratic Senator Chuck Schumer said that the administration had done the right thing by bringing new leadership to the Secret Service.

"The series of breaches has been serious and hard to explain. They need to get to the bottom of it quickly and fortunately, this process has now begun."

The White House said that Obama, who says he has full confidence in agents who protect him, called Pierson on Wednesday afternoon to thank her for 30 years of dedicated service.

The Gonzalez incident and the elevator breach proved to be catalysts for Pierson's departure.

Stunning, repeated failures

The 42-year-old Iraq veteran's intrusion triggered widespread incredulity, with lawmakers demanding to know how someone could scale an iron fence, race 70 yards (meters) across a lawn, enter an unlocked White House front door, knock down an agent and run into the East Room without being stopped.

Gonzalez was ultimately tackled by an off-duty Secret Service officer who was walking through the premises, according to reports. A search of his car later revealed hundreds of rounds of ammunition.

A string of security alerts around Obama have forced the Secret Service onto the defensive in recent years, including the firing of shots at the White House which struck the building in November 2011.

Secret Service agents were also embroiled in a 2012 prostitution scandal in Colombia ahead of a visit by Obama, while drunk agents in the Netherlands last March were also censured.

The 2011 shooting incident was the subject of a recent Washington Post report highlighting that it took four days for the Secret Service to determine that the White House was struck by gunfire while one of Obama's daughters was inside.