The Washington Post reports: The timing of the resignation has caused a controversy, with members of Congress and others questioning why the disclosure was not made until after Tuesday’s election. Some have also complained that the FBI did not notify the White House and senior members of Congress earlier that the CIA director was under investigation.

The law enforcement officials did not provide an exact timeline for the investigation, but they said that the inquiry started at least several weeks ago. They said investigators thought they were dealing with a routine harassment case until they discovered the e-mails were traced to a private e-mail account belonging to Petraeus.

The initial concern was that someone had broken into the CIA director’s e-mail account, leading to concerns about potential security breaches, according to the officials. As the investigation proceeded and more e-mails emerged, along with [Paula] Broadwell’s role, FBI investigators realized they had uncovered an affair between Petraeus and Broadwell, the officials said.

The investigators first interviewed Petraeus about two weeks ago, the officials said. Petraeus was told at the time that no criminal charges would be forthcoming and the idea of him resigning was not raised, the officials said.

One of the law enforcement officials said Justice Department officials were unclear on what steps to take next because they had determined that there had been no crime and no breach of security.

It was not until Tuesday that the Justice Department notified James Clapper, the director of national intelligence, that compromising material about Petraeus had been uncovered as part of an investigation, according to a senior intelligence official. Clapper then spoke with Petraeus and told him to resign.

“Director Clapper learned of the situation from the FBI on Tuesday evening around 5 p.m.,” the intelligence official said. “In subsequent conversations with Director Petraeus, Director Clapper advised Director Petraeus to resign.”

The official declined to say whether Petraeus had considered resigning at that point, but he said it was quickly clear to Clapper that stepping down was “the right thing to do” for Petraeus.

The official said that Clapper has been fully briefed on all aspects of the FBI investigation and has not called for the DNI or CIA to conduct a follow-on probe or damage assessment — indicating that Clapper does not see the case as a security threat.