Speaking on the BBC’s Good Morning Scotland programme on Friday, Mr Mundell said that the level of “politicking” by opposition parties over Brexit could not have been anticipated by the Prime Minister.
On Friday afternoon, MPs will be asked to vote on Mrs May’s Withdrawal Agreement.
Last week, House of Commons Speaker John Bercow told Mrs May that he would not allow the same deal to be brought back to Parliament for a third vote unless changes were made, after it had already failed twice.
Unlike on the two previous occasions where MPs voted down the deal, this time the only element which MPs will vote on is the Withdrawal Agreement - leaving out the political declaration part of the deal.
In a series of indicative votes on Wednesday, MPs could not find consensus for any proposal that was put forward, although Ken Clarke’s customs union proposal came closest to securing a majority, losing by eight votes (272 to 264).
“It’s very, very disappointing that colleagues, that other parties haven’t supported the deal,” said Mr Mundell.
“I think one thing that we hadn’t anticipated was the level of politics that would be played with the deal.
“What I think she (the Prime Minister) couldn’t factor in was the level of politicking by other parties.
“It’s quite clear that throughout this process, Labour have pursued their outcome of getting a general election, bringing the government down, ahead of securing a deal in the national interest.”
As well as the opposition from other parties, Mrs May has so far failed to win over many of her own Tory MPs, including members of the European Research Group (ERG), as well as the DUP who the Prime Minister has relied on for support since 2017.
Mr Mundell said that he was disappointed that colleagues within his party had not backed the Prime Minister’s deal, although he also criticised opposition MPs.
He said: “I’m disappointed that colleagues have not supported the deal, but I’m equally disappointed that the SNP for example have not supported the deal.
“They have instead continued to obsess about independence.”
“MPs can’t have it both ways - they can’t say, ‘oh I don’t like the future relationship that the Prime Minister’s negotiated’ and then say on the other hand, ‘oh well we can’t not tie down the future relationship because we want to have a say and shape it’.”