Azerbaijan said Wednesday it had destroyed missile launch sites in Armenia that were being used to target civilian areas during the fighting over Nagorno-Karabakh.

Armenia's defence ministry confirmed that areas inside the country had been targeted, denied its forces were firing into Azerbaijan and said it now felt justified in targeting military positions inside Azerbaijan.

It appeared to be the first time Azerbaijan claimed to have hit targets inside Armenia itself since heavy fighting broke out last month between Azerbaijani forces and Armenia-backed separatists in the disputed Nagorno-Karabakh region.

The Azerbaijani defence ministry said in statements that it had destroyed a ballistic missile system and a rocket system in Armenia in separate attacks overnight on Wednesday. The systems were deployed in areas of Armenia bordering the Kalbajar district of Azerbaijan that is under separatist control, it said.

The first launch site was aiming at the Azerbaijani cities of Ganja, Mingachevir and other populated areas, it said, adding that there had been no civilian infrastructure nearby.

Armenian defence ministry spokeswoman Shushan Stepanyan confirmed military sites in the area had been hit.

"The attack was carried out based on the mere assumption that the subject equipment was allegedly going to strike at Azerbaijan's civilian settlements," she said on Twitter.

"It goes without question that this allegation is devoid of any basis... Not a single missile, shell or projectile has been fired in the direction of Azerbaijan."

In response, Armenia's military now "reserves the right to target any military installations and combat movements on the territory of Azerbaijan," she said.

Heavy fighting erupted on September 27 over Karabakh, an ethnic Armenian region of Azerbaijan that broke from Baku's control during a war in the 1990s. Clashes have continued despite a humanitarian ceasefire agreed at the weekend.

The fighting has so far been concentrated on the frontline around Karabakh, where Azerbaijani forces are facing off against separatist fighters.

But continuing clashes are raising fears of the conflict expanding into an all-out, multi-front war between the two ex-Soviet countries.