The ministry said in a statement today that the operations of Azerbaijani and Karabakh troops "have been stopped."
An Associated Press reporter in the front-line area of Azerbaijan heard shelling this morning but there was no sound of fighting in the early afternoon.
Earlier, the Azeri government said 16 Azerbaijani troops and one civilian were killed in the past two days of fighting against separatists in Nagorno-Karabakh.
Fighting in what had been a dormant conflict erupted over the weekend with each side blaming the other for the escalation and using heavy weaponry.
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The conflict is fueled by long-simmering tensions between Christian Armenians and mostly Muslim Azeris. Armenia, although supporting the separatists, insists that its army does not engage in the fighting.
Azerbaijan's defence ministry said Karabakh militia had continued to shell its positions Monday night.
In Terter, an Azerbaijan front-line town over 300 kilometres west of the capital Baku, artillery salvos were heard late yesterday.
The region's chief, Mustagim Mammodov, said Tuesday that a 16-year-old girl was killed in shelling in the village of Hasangaya, south-west of Terter, a third civilian victim since the fighting broke out.
The numbers of casualties claimed by both sides have varied greatly since the fighting erupted since Saturday, with both Azerbaijan and Karabakh reporting dozens if not hundreds of troops killed on the other side.
Gapanli, a village south of Terter, has been one of the hardest hit. Houses bear the marks of the recent shelling; metal doors are riddled with shrapnel, power lines are cut down, craters are seen in the yards.