Petkanov was appointed justice minister in 2005 in the Socialist-led government coalition. He is member of the junior coalition partner - the NDSV party of former King Simeon Saxcoburggotski.
Petkanov, who served as Interior Minister between 2001 and 2005, said he took the decision some time ago and found the justice portfolio "very hard, even harder than taking charge of the interior ministry."
Prime Minister Sergei Stanishev told reporters he was informed about Petkanov's intention to resign, but did not say whether he will accept it.
"In the next days I will announce my view on the efficiency of the cabinet," the prime minister said.
Stanishev, who is also leader of the Socialist Party, has come under pressure to reshuffle his cabinet after an unfolding corruption scandal implicating the economy minister and the government's chief investigator eroded support for the Socialists in recent weeks.
The scandal appeared to be the main reason for the Socialist's poor showing at Bulgaria's first EU elections on May 20.
The European Commission is expected to release next month a progress report on the EU newcomer country's fight against crime and corruption.