Interim Liberal Leader Bob Rae had argued a month ago that ministers didn't give accurate information to MPs about the true price tag for the jets.
The auditor general said in a report last month that Parliament didn't get the full picture on the costs of the jets, which are closer to $25 billion rather than the $16 billion the Tories publicized.
Michael Ferguson said members of cabinet would have known about those higher costs.
The parliamentary budget officer has also said he believes the government kept two sets of books on the cost of the fighter jets.
Speaker Andrew Scheer says there isn't enough evidence that the ministers intentionally misled the Commons, and so rejected Rae's question of privilege.
But Scheer noted that a the Commons public accounts committee is studying the issue of the costs and could turn up new evidence.
"I remind the House that a determination that breach or privilege is not (evident) at this time in no way interferes with the right of any honourable member to raise a new question of privilege should the committee arrive at findings that shed new light on this matter, or should other pertinent information become available," Scheer said.
Scheer had also rejected Rae's contention that Parliament had been misled when ministers said they agreed with Ferguson's findings, but the departments said they didn't agree with certain conclusions in the report.
Again, the Speaker said there was a high bar set for findings of breach of privilege, and that includes proving that the Commons was intentionally given erroneous information.
Liberal House Leader Marc Garneau said the ruling sets a precedent that allows ministers to give misleading information in the Commons.
"I think it's setting a precedent, it's strengthening a precedent, yes, and it's unfortunate because it kind of helps everybody wash their hands on that side of the House and walk away from it," Garneau said.
"But the reality is that the government on this whole business of the F-35 has contradicted itself, has been at variance with civil servants and with generals. ... So there is no accountability in the end and that's terribly disappointing."
Also on HuffPost