The director of the US secret service has resigned amid mounting criticism of her handling of security breaches at the White House and allegations of misleading public statements.

Hours after an unconvincing appearance before the House of Representatives government oversight committee, Julia Pierson tendered her resignation to the Department of Homeland Security, which oversees the elite agency.

“Today Julia Pierson, the director of the United States secret service, offered her resignation, and I accepted it. I salute her 30 years of distinguished service to the secret service and the nation,” said the Homeland Security secretary, Jeh Johnson.

Johnson said he was appointing Joseph Clancy, who retired from the secret service in 2011, as interim acting director. “I appreciate his willingness to leave his position in the private sector on very short notice and return to public service for a period,” Johnson said. Clancy, who had worked at Comcast after his retirement, was previously the special agent in charge of the secret service’s presidential protective division.

Johnson also ordered Alejandro Mayorkas, deputy secretary of Homeland Security, to assume control of the inquiry into the fence-jumping incident on 19 September that triggered the latest crisis. According to the White House, the investigation will also examine whether a broader review of the secret service is necessary.

“The president concluded that new leadership of the agency was required,” White House spokesman Josh Earnest said at a press briefing on Wednesday. “In the light of reports ... legitimate questions were raised.” Earnest said Clancy had the confidence of President Obama and the first lady, Michelle Obama, who was reportedly angered by earlier security lapses at the White House, one of which took place while her daughter and mother were in the residence.

The final straw appears to have come from a revelation that Obama was allowed to enter an elevator with an armed man during a trip to Atlanta on September 16 – something White House officials were not told about until minutes before press reports about the incident appeared on Tuesday.

“You can assume that is part of the recent and accumulating reports to which I am referring,” Earnest said when asked if this was the decisive factor in the president withdrawing his previous support for Pierson.

Earnest confirmed that White House officials were not previously told of the security lapse, which involved a security contractor with a criminal record who reportedly behaved oddly, and said such a lapse in normal vetting procedures would be “unacceptable” if true.

“I think it’s in the best interest of the Secret Service and the American public if I step down,” Pierson said in an interview with Bloomberg News. “Congress has lost confidence in my ability to run the agency. The media has made it clear that this is what they expected.”

Ironically, Pierson had been put in charge of the secret service only last year in response to a series of scandals, including the discovery of a drunken agent passed out in a hotel during a presidential trip to Amsterdam and agents allegedly visiting prostitutes on a visit to Colombia.

Previously Pierson worked as chief of staff at the agency, overseeing new IT implementation, but also worked as a special agent herself.

Pierson’s fate is likely to have been sealed by misleading statements that the secret service issued after the fence-jumping incident, in which it was implied that the intruder was unarmed and made it no further than the front door, whereas in fact he allegedly carried a knife and ran some distance into the building.

Republicans, led by Utah congressman Jason Chaffetz, had been scathing of her handling of the incident, but anger was growing on both sides of aisle. New York Democrat Chuck Schumer was expected to become the first Democratic senator to call for her resignation in a press conference due later on Wednesday.

Elijah Cummings, ranking Democrat on the House oversight committee, said he backed the appointment of an independent panel to look at the secret service.

“As I told Ms Pierson in our phone call earlier today, we appreciate her 30 years of service to our nation, to the secret service, and to multiple presidents,” he said in a statement issued after her resignation became public.

“I absolutely respect her decision, and now we have to ensure that we focus on the difficult work of fully restoring the secret service to its rightful status as the most elite protective service in the world. I am pleased that Secretary Johnson has agreed with our suggestion to establish an independent panel of outside experts to begin to review these issues, which is a critical step.”

Cummings had previously come close to calling for Pierson to resign, saying there was little chance she could do enough to warrant staying. “I want her to go if she cannot restore trust in the agency, and if she cannot get the culture back in order,” Cummings had said during an interview on CNN. “I told her that she’s got a tall order there.”

Earlier on Wednesday, Omar Gonzalez, the army veteran accused of breaking into the White House on 19 September, pleaded not guilty to three criminal charges relating to the incident.

Lawyers for Gonzalez, who is said to suffer from post-traumatic stress disorder after serving as a sniper in Iraq, are expected to defend the case on grounds of diminished responsibility.

A grand jury indictment unsealed on Tuesday charges Gonzalez with three offences: entering a restricted building, carrying a deadly weapon, and possessing ammunition without registration.

Prosecutors claim Gonzalez was found with a Spyderco vg10 knife on him as he was wrestled to the ground in the East Room of the White House after scaling the perimeter fence and breaching an estimated five layers of security protection.

They also allege that a search of his nearby car after the incident yielded shotgun shells and bullets for seven different calibres of firearms.