The BND chief was criticised for not reporting the affair
German Foreign Minister Frank-Walter Steinmeier has apologised to his Afghan counterpart for actions by Germany's foreign intelligence service, the BND.
German media reported last week that the BND had spied on the Afghan trade minister and a German journalist.
An Afghan Foreign Ministry spokesman said the apology had been accepted.
The BND could face legal action over claims it spied on Suzanne Koelbl, a reporter for Der Spiegel, and Afghan trade minister Amin Farhang in 2006.
Der Spiegel said the head of the BND, Ernst Uhrlau, had apologised to Ms Koelbl for monitoring e-mails to Mr Farhang.
But the magazine said that it was still considering legal action against the agency.
Mr Farhang says the BND has endangered his life.
The agency has not commented publicly on the case.
It is alleged to have installed Trojan spyware on Mr Farhang's computer hard disk in 2006.
A German parliamentary committee investigating the affair condemned the fact that Mr Uhrlau had not informed the government or the committee about the case. But it stopped short of calling for his resignation.