Mr Henderson, 42, was detained in the Bakassi peninsula, a sensitive border region on the Cameroon border, some time between 23 December and 6 January.
British consular officials were denied access to the financial controller, who has more than 10 years' experience of working in Africa.
Hopes rose last week that he would be freed - only to be dashed as the Nigerian authorities continued to keep Mr Henderson, of Chapel of Garioch, Aberdeenshire, in prison.
But yesterday the Foreign Office announced he had been released and appeared to be in good health.
"We are very pleased to report that Bruce Henderson has been released and is now at the High Commission in Lagos," a spokesman said.
"He seems to be in good health although [he] will be undergoing tests."
The spokesman added that British diplomats would continue to press their Nigerian counterparts on why Mr Henderson had been denied access to consul officials.
That was an improvement on the initial diplomatic exchanges on the affair. Nigerian representatives in London had denied all knowledge of Mr Henderson but then said that if he was in fact in Bakassi he was "either a mercenary, a spy, or without sense".
The affair placed considerable strain on relations with the West African state, which was suspended from the Commonwealth in 1995 following the execution of the activist Ken Saro-Wiwa and eight others.
From her home in Chapel of Garioch, near Inverurie, Aberdeenshire, Mr Henderson's wife, Carol, said: "I can't believe it, it has come from nowhere, after all the disappointment of last week, it's wonderful.
"I spoke to him about five minutes ago, he says he is well. He is very confused, but is looking forward to coming home."
"He is totally unaware that he has been on the television and in all the papers."
Mrs Henderson described how she had gone to the local school to tell her two younger children Craig, 10, and seven-year-old Lindsay.
"They were delighted - my little girl just said `Yessss', but Craig was a little more emotional and tears came into his eyes," she said.
Her husband was with the British High Commission in Lagos yesterday where he is currently being "debriefed", she said.
Mrs Henderson is unsure when her husband - who was working on a rainforest project in the Korup national park in Cameroon - will return.Reuse content