The new television and online services also involve BBC Scotland
The UK Government has been accused of trying to impose itself on a new Gaelic service which has received £12.4m of Scottish Government funding.
A Scottish minister has criticised former Labour MSP Alasdair Morrison's appointment as chairman of MG Alba, formerly the Gaelic Media Service.
Nationalist Linda Fabiani said the role should be politically impartial.
The Scotland Office said no attempt was made to influence the choice and said the selection process was transparent.
Mr Morrison also said the decision was taken by an independent panel of people who sit on the board for Ofcom.
Ofcom is the independent regulator and competition authority for the UK communications industries.
The former Western Isles MSP said he understood five people were interviewed for the post.
Mr Morrison's appointment, which is for a four-year period, was approved by the UK Government's Scottish Secretary Des Browne.
Ms Fabiani said: "I oppose this appointment as I believe that, as a public body and a broadcaster, MG Alba must be politically impartial.
"I have serious concerns that someone who has recently held a visible political office will be able to provide this impartiality."
Ms Fabiani said the Holyrood administration had made its concerns over Mr Morrison's appointment "very clear" to the Scotland Office.
Nationalist MP for the Western Isles, Angus MacNeil, said it was unfortunate that Mr Morrison's appointment had been "caught in the crossfire" of a political row between Westminster and Holyrood.
But, appearing not to want to stoke the row, he said he hoped Mr Morrison would do his best to make the new channel a success.
GAELIC SERVICE FACT FILE
BBC Scotland is a partner in the new service, which includes a new Gaelic television channel and online services
The BBC Trust gave its approval of the service in January
The BBC's total funding of £10.7m will consist of £7.2m already allocated to existing Gaelic services, £2.5m for new content and related spend and about £1m for distribution costs
Mr MacNeil said: "It is Edinburgh that is providing £12m for this channel but unfortunately Westminster making the appointment, so this has perhaps sort of been Westminster trying to impose its will on the finances of the channel."
He added: "But we have to leave that to one side and hope the channel works well and becomes a channel we can all be proud of."
The Scotland Office said appointments to the board of MG Alba followed an independent and transparent process.
A spokesman said: "We refute the ill-informed inference that the Scotland Office has attempted to influence this process in the strongest possible terms.
"If there is a row between Holyrood and Westminster over this issue, it has definitively not been set in motion by Westminster.
"The Scotland Office or its ministers were not involved in any part of that independent selection."