The court accused Rasul of "insulting" Iraq's armed forces, which is forbidden by Iraqi law.
On Monday, Iraqi Prime Minister Haider al-Abadi, also the commander-in-chief of Iraqi forces, ordered government forces to enter the oil-rich Kirkuk province in northern Iraq to regain control of the ethnically-mixed disputed areas.
However, the warrant against Kosrat Rasul is unlikely to be executed, as the central government in Baghdad has no enforceable authority in the Kurdish-administered north. Kurdish forces, which had seized the area when the Iraqi army melted away during the Islamic State group's rampage across the country's northwest in 2014, withdrew after brief clashes.
Oil prices have risen again on Wednesday, staying firm as reports of a sustained push by Iraqi forces deeper into territory once held by Kurdish separatists since the fall of Saddam Hussein in 2003.
"This department and the Iraqi federal government are the only two bodies with whom agreements should be reached for the development and investments in the energy sector", the ministry said in a statement, without mentioning Rosneft by name.
Kayhan added, "The main reason [for giving the control of Kirkuk to Iraqi forces] was the mission that the Iraqi government had previously given to peshmerga Kurds for fighting Daesh [Islamic State], and had asked them to come to Kirkuk to prevent Daesh from advancing further".
Altun Kupri likes just outside the boundary of the Iraqi Kurdish autonomous zone. "Many Iraqis were therefore shocked by the unilateral action of some elements of the Kurdish leadership - key architects of the 2005 Iraq Constitution, which enshrines and protects Iraq's federalism - in holding an illegal referendum last month".
Recoverable oil reserves at the five blocks are about 670-million barrels, Rosneft said, calling the estimate "conservative".
Rosneft announced on Wednesday that it had signed production sharing agreements for five oil blocks in Iraqi Kurdistan.