Any reports made would now not be investigated or followed up as the hotline had been closed, a spokesman said.
UFO experts expressed anger at the decision.
MoD chiefs made the decision to close the £50,000 a year department, established in 1950, after deciding there was no benefit investigating sightings which were “an inappropriate use of defence resources”.
It comes after the team was moved from the MoD’s team, similar to the FBI team featured in the TV programme the X Files, was moved a year ago from the Whitehall Headquarters to the RAF Command in High Wycombe, Bucks.
After an application under the Freedom of Information Act, the MoD admitted that responding to every UFO sightings “diverts MoD resources from tasks that are relevant to Defence”.
No decision was announced and the disclosure was instead buried on its website earlier this month.
It said that in more than 50 years “no UFO report has revealed any evidence of a potential threat to the United Kingdom”.
After investigation, around 5 per cent of reports remain unexplained.
“The MOD has no opinion on the existence or otherwise of extra-terrestrial life,” the spokesman said.
“The MOD has no specific capability for identifying the nature of such sightings.
“Accordingly, and in order to make best use of Defence resources, we have decided that from the 1 December 2009 the dedicated UFO hotline answer-phone service and e-mail address will be withdrawn.”
He added: “MOD will no longer respond to reported UFO sightings or investigate them.”
Nick Pope, who ran the Ministry of Defence UFO project from 1991 to 1994, said it was “outrageous”.
“We’re leaving ourselves wide open to terrorist attacks,” he told The Sun.
The spokesman said the programme to release departmental files on UFO matters to the National Archive would continue.