Prokop entered conservative Chancellor Wolfgang Schuessel's government as interior minister in 2004. During her tenure, Austria tightened rules for foreigners in the country and made it more difficult for refugees to be granted asylum.
Prokop had said she was ready to continue serving in a ''grand coalition'' government, which her conservative party and the centre-left Social Democrats have been trying to hammer out since Austria's October 1 general election.
The two parties last month set themselves the goal to finalise the talks and swear in a new government by January 11.
Schuessel and President Heinz Fischer were expected to decide later today who would replace Prokop or take on her duties for an interim period.
Prokop entered regional politics in 1969 after winning a silver medal in the women's pentathlon at the Olympic Games in Mexico City 1968.