Pete Cammarano insisted under oath Tuesday that his boss, Gov. Phil Murphy, was kept out of the loop about allegations of sexual assault swirling through his administration.

Cammarano, Murphy's outgoing chief of staff, seemed intent on dispelling the cloud of doubt hovering over Murphy since 31-year-old Katie Brennan's accusations rocked his administration two months ago.

"There are times that I wish that I told the governor,'' he testified before a joint legislative panel in Trenton, which is investigating the Murphy administration's bungled response to Brennan's allegations that she was raped by a Murphy aide during the governor's campaign in 2017.

Yet Cammarano's testimony produced more questions than answers about the scandal that threatens Murphy's credentials as a #MeToo movement champion; as the progressive governor who boasts of a historic hiring of women for his Cabinet.

The testimony raises serious, lingering questions about why the administration hired former aide Al Alvarez despite troubling allegations surrounding him. And why did they take so long to remove him from the public payroll when it was clear that he was a liability?

"Obviously there are lot of gaps that took place that nobody followed up on,'' said Sen. Loretta Weinberg, D-Teaneck, co-chairwoman of the investigative panel.

We learned, for example, that Murphy administration officials didn't seem to be in any rush to cut ties with Alvarez, whom Brennan accused of sexually assaulting her in her Jersey City apartment in 2017 after a social gathering of campaign supporters and aides.

MORE:Who is Katie Brennan? She tells lawmakers her story in Phil Murphy hiring investigation

MORE:Top Murphy officials failed to fire staffer accused of sexual assault, witnesses say

After Brennan personally detailed the allegations in March to Matthew Platkin, Murphy's chief counsel, Cammarano told Alvarez that he "should make arrangements to leave" his post as chief of staff at the Schools Development Authority. Alvarez denied the allegations and got "teary-eyed and emotional,'' Cammarano testifed.

But Cammarano said he believed Alvarez "understood my instruction that he was to leave state service."

Apparently, he didn't.

Alvarez had to be told a second time. Ten weeks later, in early June, Schools Development Authority director Charles Mckenna told Alvarez that he should "step back" from state government work. McKenna, a holdover from Republican Gov. Chris Christie, was ordered by Platkin to urge Alvarez out the door.

Platkin's order came days after a frustrated Brennan emailed Murphy and his wife Tammy, asking for an audience to discuss a "sensitive matter" that happened during the campaign. She did not mention the sexual assault allegations.

"He seemed to understand,'' McKenna testified Tuesday as he described his June meeting with Alvarez. "He said that he didn’t do anything wrong but he didn’t want to put the governor in a bad position."

Yet Alvarez didn't resign until Oct. 2, when The Wall Street Journal contacted the administration for comment on a lengthy story it was writing about Brennan's allegations. Murphy and his wife "were blindsided and completely shocked,'' Cammarano testified.

The question lingers: Why did top administration officials take such a squishy, passive-aggressive approach to the firing of an "at-will" employee who loomed as a political and public relations disaster for Murphy?

It is worth noting that the Hudson County Prosecutor's Office investigated Brennan's allegations last year and chose not to charge Alvarez, who had served as director of Latino and Muslim outreach for Murphy's gubernatorial campaign.

Murphy's transition officials became aware last December that Alvarez had been investigated, although they were unaware that Brennan was the accuser, according to Cammarano's testimony. They ordered a background check. When it came back "clean,'' Alvarez was offered a job.

But a furious Brennan, a campaign volunteer who became chief of staff at the New Jersey Housing and Mortgage and Financing Agency, testified last month that she was not going to stay silent until Alvarez left his job and until the Murphy administration enacted hiring reforms.

Platkin, who is expected to testify early next year, was clearly aware of the political danger. Platkin told McKenna that if Alvarez resisted his suggestion to leave, McKenna was to warn Alvarez that "it could become ugly or embarrassing for the governor, McKenna testified.

McKenna said Christie would never have let an employee who had a cloud of sexual misconduct over his head remain on the payroll.

"There was certainly a bright line for the governor I worked for when it came to something like this," he testified.

Lawmakers struggled to conceal their frustration — and confusion.

“I don’t understand that level of dysfunction that takes six, seven months for it to come to a close,” Sen. Teresa Ruiz, D-Essex, told Cammarano, referring to Alvarez's drawn-out departure.

“It’s something that I look back on and try to figure out, you know, why did that happen, and I don’t have the answer to it,” Cammarano responded.

Now, the joint legislative panel will spend the next couple of months looking for that answer — and for answers to other thorny questions that might not go away so easily.