The Foreign Office (FO) on Tuesday cautioned Tehran that a warning issued by the Iranian army chief a day earlier was against the "spirit of brotherly relations" between Pakistan and Iran.

Read more: Iran warns will hit 'militant safe havens' inside Pakistan

The FO summoned Iranian Ambassador Mehdi Honardoost to convey Pakistan's concerns regarding a warning issued by Maj Gen Mohammad Baqeri that Tehran would hit 'militant safe havens' inside Pakistan if the government did not confront militants who carried out cross-border attacks last month.

"We expect Pakistani officials to control the borders, arrest the terrorists and shut down their bases," Baqeri had said on Monday. "If the terrorist attacks continue, we will hit their safe havens and cells, wherever they are," he added.

During his meeting with the ambassador, FO Spokesperson Nafees Zakaria, highlighting an improvement in bilateral relations between the two countries, urged Iran to refrain from making statements that would harm relations, according to the statement.

Zakaria said an agreement had already been reached to "enhance cooperation on border issues" during the visit of Iranian Foreign Minister Javad Zarif on May 3.

Zarif in his visit had asked Prime Minister Nawaz Sharif to improve border security, and Pakistan had assured Iran it would deploy additional troops along its border.