Finance Secretary Kate Forbes claimed regions such as the Highlands risk losing out in a row over major infrastructure spending in Scotland.
Ms Forbes said there is a lack of clarity with UK Government plans to “level up” parts of the country with extra investment.
The two administrations in Edinburgh and London have also argued over “connectivity” plans.
Conservatives want to replace EU funds by investing directly in projects such as trunk roads, but the SNP claim that undermines devolution and could lead to Holyrood’s budget being cut.
Ms Forbes, appearing before MPs on the Scottish Affairs Committee, compared the concerns with positive collaboration on regional and city deals.
‘Undermined’
Both governments have praised efforts to work on community plans such as Tay Cities, Inverness and Highlands, and Aberdeen and Aberdeenshire.
But on wider issues, Ms Forbes said the SNP Government were “excluded” and respect is “eroding”.
In the Highlands, she said EU money had helped the region disproportionately.
She added: “If city deals have demonstrated an effective way of working because there has been transparency, clarity and mutual respect – then that is somewhat juxtaposed with the approach that’s been taken now where we are certainly cut out of the knowledge about the process will work with levelling up or shared prosperity.
“That undermines all of our ability to make wise plans for investment.”
Scottish Conservative leader Douglas Ross, who is also an MP, said it was the SNP government that prevented officials from taking part.
It emerged last year that Transport Scotland officials were told “not to engage” with the UK Government, sparking a row with the Scottish Secretary.
Ms Forbes said the UK Government started the process and laid the ground work without any input from Holyrood.
‘More efficient’
“On the union connectivity review, or levelling up, or shared prosperity, or take your pick of a number of different alternative UK Government funding streams, the Scottish Government has not been party, and has not been included in the process of establishing those funds or in terms of how projects will be analysed for those funds,” she said.
Mr Ross demanded the Scottish finance secretary checks the record and writes back to the committee.
Ian Stewart, a UK minister in the Scotland Office, said the shared prosperity fund will be “more efficient” than the old EU model.
The connectivity review will bring the UK closer together, he said.