Speaking at a news conference, he said he would present his resignation to the legislature in 10 days.
He also said his Orinats Yerkir (Law-Based Party) was quitting the government coalition because of disagreements on domestic and foreign policy.
Baghdasarian has rejected Armenia's official policy of not seeking NATO membership.
The Orinats Yerkir party has recently seen a number of defections by lawmakers. All of the defectors are wealthy businessmen with close connections to the government of President Robert Kocharian.
Baghdasarian was seen in the past as one of Kocharian's possible handpicked successors.
(with material from Interfax)