Prosecutors said Nanev caused €1.24 million (2.45 million levs) of damage by signing two contracts last December with Swiss drugmaker Roche Holding AG for the delivery of the influenza drug Tamiflu.
Nanev is the first minister in the Balkan country to be charged with corruption since communism collapsed 20 years ago. He faces up to 10 years in jail if found guilty.
"It is important we have proved that there are no untouchable people," said prosecutor Nikolai Kokinov.
Prosecutors said Nanev had chosen the vaccine offered by the Bulgarian arm of Roche rather than the cheaper one on offer from Britain's National Health Service, and said they would ask the Sofia City Court to suspend him.
Prime Minister Boyko Borissov, whose centre-right GERB party came to power last July on promises to end a climate of impunity, has promised to be uncompromising when there are suspicions of corruption among his officials.
However, Mihail Mikov, a member of parliament with the Coalition for Bulgaria and a former interior minister, said Nanev is a scapegoat. Mikov claimed that Prime Minister Borissov was looking for an excuse to dismiss an unpopular member of cabinet.
Aid dependent on fight against corruption
Brussels will assess Bulgaria's progress in fighting graft and organised crime in July, and failure to show results may threaten access to some of the €11 billion in aid promised to the EU's poorest member between now and 2013.
In an interim report last week, Brussels said the new government had the political will to fight graft but criticised the lack of convictions.
A number of former ministers and high-ranking officials have been prosecuted, but Bulgaria has so far convicted only one former senior official of graft and has jailed just one crime boss.
Punishing officials within GERB's ranks found guilty of fraud is a vital test of the new cabinet's anti-graft drive, EU diplomats have said.
Prosecutors have charged three ministers in the previous Socialist-led government with corrupt practices and arrested members of powerful crime gangs since the new cabinet came to power but no trial dates have been set yet.
Borissov has put more pressure on the inefficient and graft-prone judiciary to wrap up a number of high-profile trials, which Brussels and the Bulgarian public see as a test of the government's ability to rein in corruption.
On Monday (29 March), a Sofia court sentenced six Bulgarian businessmen to jail for laundering €7.5 million in EU farm aid in one of the closely-watched trials.
(EurActiv with Reuters.)
