Peter Box told his Cabinet on Tuesday that hopes for a region-wide agreement, which would have seen an unprecedented transfer of powers from Westminster to Yorkshire had been ended.
A meeting between Communities and Local Government Secretary James Brokenshire and senior councillors on Friday was described as "very positive" by the Yorkshire leaders afterwards.
In a statement, they said they remained committed to a mayor-led One Yorkshire agreement.
But today Coun Box said such a deal was unlikely to be made a reality.
He told the Cabinet: "I attended a meeting on Friday with the Secretary of State, James Brokenshire.
"He was his usual unfailingly polite self, but he made it quite clear, 100 per cent clear in fact, that One Yorkshire was not supported by the government.
"He set out the criteria that the government had used in coming to that decision, and he explained that One Yorkshire didn't meet that criteria.
"He did agree to meet us later this year to discuss alternatives to a One Yorkshire deal, and I will report back to council what I'm told about that."
Coun Box said last July that he would continue to support leaders who wanted region-wide devolution but warned them against "banging our heads against a brick wall forever" because of the government's reluctance to approve it.
As a result, he said he would pursue an exclusive district-wide deal for Wakefield, to confront challenges posed to the area by potential job losses to robots.
Last week, Coun Box said that work to secure such a deal was ongoing.