Welsh Secretary Simon Hart said there is a "significant" number of coronavirus vaccines being held up in Wales' health system which could have already been administered.
Mr Hart said 300,000 vaccines had been delivered to Wales but the latest figures show just 112,973 people have received their first dose.
Welsh Affairs Committee chairman Stephen Crabb MP (Preseli Pembrokeshire) asked Mr Hart whether there was a supply problem getting vaccines to Wales from the UK Government, after he was told supplies of vaccines had not arrived at a surgery in his constituency.
Mr Hart said: "Somewhere in the system in Wales there is a significant balance, even as we speak, of vaccines which have been delivered and haven't been issued to either GP surgeries or other clinical settings where they might be administered.
"So I don't know why that is the case. All I do know is that the 300,000 vaccines have been delivered. And yet only roughly a third of those have been administered. I'm not in a position to answer why that might be."
The Welsh Government has faced criticism in the past week for vaccinating fewer people in proportion to its population than the other home nations.
The House of Commons Welsh Affairs Committee heard that in Wales the ratio of people receiving the first dose of the vaccine per 100,000 was 3,215.
This compared to 3,514 in Scotland, 4,005 in England and 4,828 in Northern Ireland.
The Welsh Government has set out an aim to vaccinate the top four priority groups by mid-February - that's all care home residents and staff, frontline health and social care staff, anyone aged over 70 and everyone classed as clinically extremely vulnerable.
They plan for more than 100 GP practices to be running vaccination clinics by January 15. This will increase to 250 before the end of the month.
The Welsh Government has previously said the shortfall in the number of jabs administered was because it had been stockpiling vaccine for a second dose before the scientific advice changed.
Wales' health minister told ITV News that the "logistical challenges are largely behind us" and Wales is making "rapid progress."
Vaughan Gething said: "I understand why some people are worried but you can be confident Team Wales won't leave people behind and our NHS will get this job done for all of us."
Mr Hart also said he was "sorry" after the Treasury wrongly announced Wales would be receiving £227 million in additional coronavirus support.
He told the Welsh Affairs Committee that the figure "was not new money" and was instead included in the £5.2 billion Covid recovery funding already committed to Wales.
Mr Hart said: "I accept with a degree of humility that these messages aren't always perfect first time. I realise that did cause some confusion.
"But I'm hoping, taken in the context of the overall financial contribution made across the whole of the UK to try and help people through this crisis, that everyone understands there's no malice intended in that."
He added: "It is important to stress that was not new, and I'm sorry if anybody got the impression that it was new money."