The Independent Police Complaints Commission said Operation Midland was "extensive and carried out diligently".
There was no evidence to indicate "bad faith, malice or dishonesty" by the officers, the watchdog said.
The much-criticised operation closed last March without a single arrest.
Of five officers referred to the Commission, three were cleared of causing "prolonged and undue stress" to those being investigated.
One of the three - an unnamed detective chief inspector - is being investigated over an alleged failure to present relevant information to a judge when applying for a search warrant.
Former MP Harvey Proctor, who was among those cleared of being part of an alleged Westminster abuse ring, said the "bungled and disastrous" police operation had ruined his life and left him destitute.
He said he believed no police officer would ever be held responsible for it, and accused the IPCC of conducting a "whitewash".
The Â£2.5m Met investigation was launched in 2014 after a man known as "Nick" claimed that boys had been sexually abused and even murdered by a group of powerful men from politics, the military and law enforcement agencies.
The abuse was said to have been carried out at locations across southern England and London in the 1970s and 1980s.
Retired judge Sir Richard Henriques reviewed the investigation and identified 43 serious failings in his report, including that "Nick" had been believed for too long and that search warrants had been applied for with flawed information.
Former Met Police commissioner Sir Bernard Hogan-Howe apologised to those affected by the inquiry, including Mr Proctor, former military chief Lord Bramall, and the wife of the late Lord Brittan, a former home secretary.
The force referred five officers to the IPCC.
The IPCC has now cleared three of them - Deputy Assistant Commissioner Steve Rodhouse, Detective Superintendant Kenny McDonald and an unnamed detective chief inspector - of causing prolonged and undue stress to those under suspicion by failing to properly investigate "Nick's" claims.
Mr McDonald had, at one stage, publicly described "Nick's" allegations as "credible and true".
In a statement, the IPCC said: "There is no evidence to indicate bad faith, malice or dishonesty and no indication any of the officers may have behaved in a manner which would justify disciplinary proceedings.
"The information available indicates the investigation was extensive and carried out diligently with the majority of the decisions made appropriately recorded."
But the watchdog said there was an indication that the DCI and two other detectives may have failed to accurately present all relevant information to a district judge when applying for search warrants for three properties.
The searches - in March 2015 - resulted in those under suspicion being named in the media.
The IPCC said it was discontinuing its investigation into allegations of irregularities in the seizure of exhibits during the searches.
There will also be no further investigation of Mr Rodhouse for his conduct in relation to a separate inquiry involving Lord Brittan.
IPCC commissioner Carl Gumsley said: "The allegation that incomplete information may have been provided to a district judge when applying for search warrants is serious and the IPCC will thoroughly investigate this matter."
Three senior Scotland Yard officers have been cleared over their handling of allegations at the centre of an investigation into VIP paedophile claims, the police watchdog has said.