The Irish premier said he has “some difficulties” with the new rules that will allow for smooth post-Brexit trade between Northern Ireland and Britain, but that they do not cross any red lines.
Leo Varadkar also said the command paper, titled Safeguarding The Union, contains negative language.
The document, published on Wednesday, contains details of the agreement between the UK Government and the DUP which paved the way for the party to end its boycott of the power-sharing institutions in Northern Ireland.
The measures remove checks on goods travelling from Great Britain that are to stay in Northern Ireland.
The Northern Ireland Assembly is due to meet tomorrow.
Speaking in Dublin on Friday, Mr Varadkar said: “I think it’s really good news that the Assembly and the Executive will be back up and running on Saturday. Fingers crossed that nothing goes wrong between now and then.
“I really look forward to working with the new First Minister and the new Deputy First Minister, and the new Executive, on issues of common interest.
“I’ve read the command paper, I would have some difficulties with some aspects of it.
“I don’t like the negative language about the all-Ireland economy and I think it very much puts the British government in the place of being advocates of the Union, whereas in the past they’d signed up to rigorous impartiality.
“But none of those things crossed any red lines in my view.
“When Brexit happened, we set out our objectives. One was to make sure the Good Friday Agreement was respected, it has been, and there was to be no hard border between north and south, and that our position in the European Union and the single market wouldn’t be diminished, and none of those red lines are crossed.
“If this is the price, if this is what has to be accepted in order to allow power-sharing to resume, I think that’s worth it.
“There is opposition from nationalists and unionists, but I think the majority of both communities will accept this.”
Mr Varadkar said that after reading the document, there were no “red flags” raised about its details.
He said that while there are no changes to the Windsor Framework, there are some changes to how it is going to operate.
The Fine Gael leader said he spoke to European Commission president Ursula von der Leyen about the agreement when he travelled to Brussels on Wednesday and that the EU Commission will study its contents.
“Anything that results in seamless trade, whether it’s north-south or between Northern Ireland and Britain, I’m all for,” he added.
“I’ve never wanted any of these barriers in the first place – one of the reasons why I wasn’t in favour of Brexit.
“I spoke to President (Ursula) von der Leyen about this Wednesday and I know (Foreign Secretary) Lord Cameron spoke to Maros Sefcovic, the Tanaiste had some calls too.
“So, the commission is studying what was agreed between the UK Government and the DUP, so far no red flags have been raised, so far no particular concerns arise.
“I’m fairly confident that it is totally consistent with what’s been agreed previously in the Withdrawal Agreement and with the Framework, but it is the European Commission who has to make that assessment, not us as the Irish Government.”