The Dutch ambassador to Estonia, Hans Glaubitz, is leaving the country, complaining of persistent racist and homophobic abuse.
The men said they were regularly abused in Tallinn
Mr Glaubitz said he and his partner, a black Cuban man, were regularly insulted when they went out.
An Estonian foreign ministry spokesman said the men had been well received at an official level, but expressed "regret" over any public abuse.
Mr Glaubitz is to be posted to Canada to become consul-general in Montreal.
He told Dutch newspapers: "It is not very nice to be regularly abused by drunken skinheads as a 'nigger' and to be continuously gawped at as if you have just stepped out of a UFO."
While the Netherlands has a reputation as one of the most liberal countries in Europe, having legalised same-sex marriage in 2000, Estonia has "not really gone through the enlightenment revolution", according to Rainer Kattel, professor of political science from Tallinn University.
"Estonia does have latent racism, but it is not violent like in other countries. If you are openly gay and of a different race people will make mean comments to you," he said.