Mr Trump had the option of appealing against the decision
The Scottish Government has been accused of undermining Aberdeenshire councillors over Donald Trump's planned £1bn golf resort.
The claim came as MSPs on the economy and tourism committee praised the decision to "call in" the application.
They said it was a project of huge national importance for Scotland and should be decided by ministers, not a local council.
Some Aberdeenshire councillors who rejected the plans criticised the move.
The project's potential was discussed by MSPs on Wednesday after the planning application was called in. The process could take months.
MSPs said Aberdeenshire Council's decision to refuse the application was sending the wrong message to the world that Scotland was not open for business.
Committee convener Tavish Scott described the Trump project as an "enormous development for Scotland".
He said the committee would stress the nationwide implications of the project, particularly in light of an inquiry it is to carry out into tourism.
Aberdeen North SNP MSP Brian Adam said: "I'm very concerned that if this development doesn't go ahead it's going to deliver an international message that Scotland is not the kind of place to come and invest in."
Aberdeen Central Labour MSP Lewis Macdonald added: "The bigger picture here is about the kind of message that Scotland is sending out to the world and about whether we're able to take opportunities when they arise."
One councillor who opposed the scheme, Debra Storr, demanded a public inquiry. Martin Ford, who also voted against, said the call-in was unusual.
The property tycoon's proposals were turned down last week by a council committee.
Ministers in Scotland said the development issue required consideration at a national level.
It followed The Trump Organisation's head of international development, George Sorial, saying on Tuesday the group was not currently considering resubmitting the plans for the Menie Estate near Balmedie.
Aberdeenshire Council leader Anne Robertson said the council could not overturn the decision.
The new move by the Scottish Government, thought to be unprecedented, was welcomed by Mr Trump, as well as Ms Robertson.
However, committee chairman Martin Ford, who used his casting vote to turn down the plan, said the intervention of the Scottish Government called into question the integrity of the planning system and was a "most unusual route" which raised serious concerns.
He said: "There is no doubt in my mind that the council has been bullied over the last few days and that has caused us immense difficulties.
"The result is that the application has taken a most unusual route and ended up with the Scottish ministers.
"It is inescapable that this has happened in response to the behaviour of the applicant. It calls into question the integrity of the planning system."
Mr Ford added that it was "standard practice" for applicants to appeal against the decision or resubmit a modified plan.
The plans for the Balmedie area have caused controversy
He added: "There might be a view out there that there are some applications and some applicants that we are simply not allowed to refuse.
"That is a big problem for our whole planning system."
Ms Storr said of the Scottish Government decision: "It does smack a little bit of they have got rather forced into this situation because the Trump organisation wouldn't appeal, and perhaps because they didn't like the decision of Aberdeenshire Council."
Mr Trump responded to the government's decision in a statement, saying: "Obviously this is a reaction to the unprecedented support for our Aberdeenshire development that's been received.
"I'm very honoured by this response."
RSPB Scotland director Stuart Housden said: "We call on ministers to take a cool look at this development and its impact on Scotland's priceless natural heritage."
The Scottish Government statement, issued on Tuesday evening, said: "Ministers recognise that the application raises issues of importance that require consideration at a national level.
"Calling the application in allows ministers the opportunity to give full scrutiny to all aspects of this proposal before reaching a final decision."
A Scottish Government spokesman said the speed of the decision would depend on how the application was dealt with.
A Reporter will first have to gather all the relevant information. If either the council or applicant ask for a public inquiry, there would have to be one. The Reporter could still ask for one, even without a request.
If there is no public inquiry, the application could be dealt with either by a shorter hearing process, or through written submissions. Either way, anyone who wants to contribute would have the chance.
Even if the application is dealt with by written submissions, a decision would be expected to take months rather than weeks because of the complexity of the issues.
Northern Ireland's First Minister Ian Paisley met Mr Trump in New York on Tuesday. Mr Trump is now considering buying land in County Antrim to develop the golf resort after his plans in Aberdeenshire were rejected.
The Aberdeenshire proposals were criticised by some environmental groups and local campaigners but also received backing from some business figures.