The agreement, widely known in Ukraine as the Kharkiv Pact, allowed Russia to keep its Black Sea Fleet in the Crimean port of Sevastopol.
Yanukovich, who fled to Russia in 2014 after mass protests, has already received a 13-year jail sentence in absentia for treason.
That case was related to a letter he sent to Russian President Vladimir Putin on March 1, 2014, asking him to use Russian army and police forces to restore order in Ukraine.
Yanukovich could not immediately be reached for comment.Â
He has previously denied all allegations against him.
The Ukrainian prosecutor general's office said a Kyiv court had on Monday ordered Yanukovich's arrest because the Kharkiv Pact had enabled Russia to increase the number of troops it had in Ukraine and to seize and annex Crimea in 2014.
Yanukovich's actions had violated the constitution and "to the detriment of the sovereignty, territorial integrity and inviolability of the defence, state and economic security of Ukraine, provided assistance to a foreign state".
Ukrainian investigators told Yanukovich in January last year that he was suspected of treason over the Kharkiv Pact.
Russia invaded Ukraine on February 24 and has used the Black Sea Fleet to fire at Ukrainian targets in what Putin calls a "special military operation".
