One in three Thomas Cook customers who are claiming refunds will not be paid within the 60 day target.
The aviation regulator has said customers cannot be paid until additional information has been provided, the Civil Aviation Authority (CAA) said.
More than 22,000 people have submitted online claims since Atol started the refund programme on 7 October.
Claimant have been urged to check their junk and spam folders should they not hear anything by the end of the week, the regulator said.
CAA chief executive Richard Moriarty said, “We thank consumers for their ongoing patience as we continue to do all that we can to work through the UK travel industry’s largest ever refunds programme.
“I appreciate that this is a concerning time for Thomas Cook customers who are waiting for their refunds, particularly at this time of the year.
“We will have already paid out more than £160m by this weekend and will continue to pay claims as soon as possible.
“Where we have had to request further information, we encourage those consumers to respond at the earliest opportunity so that we can finalise these payments.
“I would like to reassure consumers that all valid Atol-protected payments will be refunded.”