"If this election is a referendum about Hillary Clinton, she loses," Conway said on "Squawk Box," said days after FBI Director James Comey announced the new probe. "And now it is again a referendum on Hillary Clinton."
"I think people have been asking the right questions about the wrong candidate," Conway said, referring to criticism of Trump.
"Who really is unqualified, who's unfit to be president? Who has shown what they'd do with their national security information?" she asked rhetorically.
Authorities want to find out whether of any emails on Weiner's computer contained any classified material connected to Clinton while she was the Obama administration's secretary of state.
Conway told CNBC the "right thing" for the FBI to do is to follow wherever the investigation leads. "It's not for us to say speed it up because of the election or slow it down."
"Had [Comey] sat on this exclusive information he could very well have affected the election," she said.
Senate Minority Leader Harry Reid, D-Nev., said Comey's announcement on Friday of the investigation may have violated the Hatch Act, which bars federal government officials from using their authority to influence elections.
On "Meet the Press" on Sunday, Clinton's campaign manager Robby Mook called on the FBI to share any unreleased information relating to the Clinton email investigation.
The Clinton camp is "asking for information they're not going to get," Conway told CNBC. "Secondly, and most importantly, they're trying now to politicize the FBI."
The Justice Department opposed Comey's plan to notify Congress about the new, potentially relevant Clinton emails, sources familiar with the discussion told NBC News. In the end, Comey decided it was better not to wait until after the election to notify Congress.
Abedin has told the FBI she was unaware that any of her emails were on the laptop authorities seized as part of their investigation into Weiner's latest sextexting scandal, this time allegedly with a 15-year-old girl.