President Pervez Musharraf said the exercise was needed for technical reasons.
The medium range Hatf V missile of the Ghauri series, which can hit targets up to 1500km (930 miles) away, was earlier tested last Saturday.
"Pakistan this morning conducted a second successful test of its intermediate range ballistic missile Hatf V as part of series of tests planned for the Ghauri missile system," a military statement said.
Musharraf witnessed the test firing and said it was "not intended to send any political signals outside the country but was necessary for validation of technical parameters", the statement added.
Pakistan test-fired the Shaheen II ballistic missile with a range of 2000km in March.
Some experts say Ghauri was
developed with N Korean help
The Ghauri missile was developed by Khan Research Laboratories, Pakistan's main uranium-enrichment facility, which was named for Abd al-Qadir Khan.
Once revered as the father of the country's atom bomb, Khan was sacked this year from his job as a special government adviser after he admitted to exporting nuclear secrets to Iran, Libya and North Korea.
Some experts say the Ghauri missile was developed with North Korean help in return for nuclear know-how.