Mark Canning said he was summoned to see Indonesian Foreign Minister Marty Natalegawa, who "conveyed to me in clear terms the strong concern of the Indonesian government at the opening of a 'Free West Papua' office in Oxford".
The "Free West Papua" group last month established the headquarters in the southern English city, and the opening ceremony was attended by the city's mayor and a member of parliament.
"I explained to the minister that we recognised the sensitivity of this issue for Indonesia," said Canning in a statement.
He stressed that the opening of the office "has nothing whatsoever to do with the British government".
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At the weekend, Natalegawa issued a statement saying the office was "clearly incompatible and contrary to the friendly relations that have existed between the two countries".
The issue of separatism in Indonesia remains deeply sensitive, particularly after the bloody secession of East Timor which gained its independence in 2002.
They have demanded a referendum on self-determination for the region's estimated population of 3.6 million.
The vast area is split into two provinces for administrative purposes, Papua and West Papua, but some -- such as the group which set up the office in Oxford -- refer to the whole region as West Papua.
Indonesia has strict treason laws and courts have handed down stiff penalties from 20 years' jail to life for people caught with separatist symbols such as the Papuan flag.