Frans Timmermans indicated that not everybody on board had died instantly when the plane was hit by a missile.
According to an initial report, flight MH17 broke up in mid-air after being pierced by objects at high velocity.
Frans Timmermans has now said he regrets the remark and upsetting families.
“The last thing I want is to add to their suffering in any way,” he said in a government statement released hours after he made the comment on the Pauw talk show on Dutch TV.
“I shouldn’t have said it.”
The Dutch public prosecutor has confirmed that an oxygen mask was found, although a spokesman said it was around the passenger’s neck rather than their mouth. It has been secured with elastic and tested for DNA and fingerprints.
The plane had been flying from Amsterdam to Kuala Lumpur on July 17 when it went down over rebel-held territory. Pro-Russian separatist leaders deny shooting it down with a missile.
Although 196 of the passengers were Dutch, the passenger with the oxygen mask was not, the prosecutor said on October 9. Dutch media said the victim in question was an Australian and the family had been informed about the development.
None of the other victims was wearing an oxygen mask, the public prosecutor added. The mask was from a Boeing 777 plane, but it was unknown how and when it had been put on.
Frans Timmermans is seen as one of the big hitters in the Dutch government.
He is due to leave his post shortly as foreign minister to take up a post as European Commission President Jean-Claude Juncker’s right-hand man.
He mentioned the oxygen mask during an interview with Jeroen Pauw, in which he was taken to task for an emotive speech he gave to the UN four days after flight MH17 was downed on July 17.
In his address to the Security Council, Frans Timmermans imagined the horror felt by the passengers “when they knew the plane was going down” and wondered whether they had looked each other in the eyes “one final time, in an unarticulated goodbye”.
He acknowledged that those on board would not have seen the missile hit the plane.
“But do you know that someone was found with an oxygen mask on their mouth – and so they had the time to put it on?” Frans Timmermans said.
He went on to say that nothing could be ruled out about the 298 victims’ final moments.
The official inquiry into the MH17 disaster had not made any mention of an oxygen mask being found on one of the victims.
However, several experts concluded that the plane would have disintegrated too quickly for the passengers to have known anything about it.
Victims’ families, angry that they had not been told about the oxygen mask before, were told by prosecutors that an inquiry was still being carried out and no conclusions had been drawn.
Although investigators were unable to visit the crash site because of fighting in the area, their initial report pieced together photographic evidence of the wreckage as well as cockpit and air traffic control data.
They said it pointed to “an in-flight break up” and added there was “no evidence of technical or human error”.
Malaysia Airlines plane was hit while flying at 33,000ft (10,000m) and debris was found over a wide area of eastern Ukrainian territory held by pro-Russian rebels.
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