There is no case for keeping the Scotland Office a decade after devolution, SNP ministers have said.
The SNP administration prefers to deal directly with Whitehall
Holyrood's Deputy First Minister Nicola Sturgeon told a Commons inquiry the institution belonged to a past era.
But Scotland Office Minister David Cairns attacked her "continuing obsession" with fostering bad relations between the two governments.
Sir John Elvidge, Scotland's top civil servant, said the office's role had moved into "different territory".
The Scottish Government told MPs that relations with the department were good, but preferred to deal directly with Whitehall.
Ms Sturgeon was giving evidence to the House of Commons justice committee, which was in Edinburgh taking evidence on its devolution inquiry.
She said the Scotland Office, headed by Scottish Secretary Des Browne, had "next to no" policy responsibilities.
Direct dealings could be carried out, she argued, through the use of joint ministerial committees, which have not met since 2002.
"Although it is important that some of the functions of the Scotland Office continue to be carried out and it is important that reserved government knows what devolved government is doing, I think that co-ordination could be carried out in different ways," Ms Sturgeon said.
"I don't think there is a case for retaining the Scotland Office and the secretary of state as separate entities."
Pointing out that half of public spending in Scotland was by UK Government departments, Mr Cairns said: "It is typical of the arrogance of the minority administration that they believe that their narrow party interest is identical with the interest of Scotland.
"In recent months, our efforts have secured UK legislation to protect whisky - one of our most important exports internationally - and working with the [Scottish] Executive, our representations secured the continuation of the innovative Fresh Talent Initiative."
Sir John told the committee he did not think of the office as a "key interlocutor in making contact work" with Whitehall.