The defence ministry statement did not specify Pakistan but said the strikes on Saturday were conducted "beyond the 'hypothetical line'" - an expression used by Afghan authorities to refer to a border with Pakistan that they have long disputed.
"Several points beyond the hypothetical line, serving as centres and hideouts for malicious elements and their supporters who organised and co-ordinated attacks in Afghanistan, were targeted in retaliation from the southeastern direction of the country," the ministry said.
Asked whether the statement referred to Pakistan, ministry spokesman Enayatullah Khowarazmi said: "We do not consider it to be the territory of Pakistan, therefore, we cannot confirm the territory, but it was on the other side of the hypothetical line."
Afghanistan has for decades rejected the border, known as the Durand Line, drawn by British colonial authorities in the 19th century through the mountainous and often lawless tribal belt between what is now Afghanistan and Pakistan.
No details of casualties or specific areas targeted were provided.
The Pakistani military's public relations wing and a spokesperson for the foreign ministry did not immediately respond to requests for comment.
Afghan authorities warned on Wednesday they would retaliate after the Pakistani bombardment, which they said had killed civilians.
Islamabad said it had targeted hideouts of Islamist militants along the border.
The neighbours have a strained relationship, with Pakistan saying that several militant attacks that have occurred in its country have been launched from Afghan soil - a charge the Afghan Taliban denies.
