The missile, Hatf VII Babur, has a range of 500km, and was fired early on Thursday. The launch site was not disclosed.
"By the grace of Allah, all design parameters for the flight were validated," a military statement said.
The Foreign Ministry said Pakistan did not inform India, as an agreement formalised between the two countries over the weekend in New Delhi on pre-notification of missile tests did not cover cruise missiles.
"The agreement on pre-notification of ballistic missiles, which has been finalized but yet not signed in New Delhi, does not cover pre-notification of cruise missile tests," said Pakistani Foreign Ministry spokesman Mohammed Naeem Khan.
The missile test agreement is part of confidence-building in a peace process between the South Asian rivals, who have fought three wars since their partition and independence from Britain in 1947. They also agreed at the weekend to set up a hot line next month to help prevent accidental nuclear conflict.
Cruise missiles are typically low-flying guided missiles that use jet propulsion to allow sustained flight.
The two countries are engaged in
a peace process
Army spokesman Major General Shaukat Sultan said Pakistan had joined the few countries "that can design and make cruise missiles."
According to the Federation of American Scientists, there are at least 12 countries who export cruise missiles: Britain, the United States, China, France, Germany, Israel, Italy, Japan, Norway, Russia, Sweden, and Taiwan.
India unveiled its first cruise missile, a supersonic joint venture with Russia named the BrahMos, in 2001.
Pakistan and India, which both carried out nuclear tests in 1998, often carry out tit-for-tat missile tests capable of reaching deep inside each other's territory.
In March, Pakistan test fired its longest range nuclear-capable Shaheen II missile which can reach 2000km.
India has said that it will test its longest range missile, the 3000km Agni III, by the end of the year. It already has the intermediate range Agni I and Agni II versions of the missile.
India also has the short-range ballistic missile Prithvi, the anti-tank Nag missile and the short-range surface-to-air Trishul missile in its arsenal.