Hadi, according to Yemeni official TV, sent condolences to the family of Qassem Aqlani, who was killed in drive-by shooting by a masked militant on a motorcycle near his house on Thursday.
"Aqlani died as a martyr after terrorists killed him," Hadi said. "The way he was killed reflects the barbarism and aggression of this outlawed group that is violating Islam and its principles that ban bloodshed."
The killing, the latest episode in an assassination campaign aimed at top military and security officials, raised concerns the country's al-Qaida offshoot is growing bolder after suffering defeats this year in a U.S.-Yemeni military offensive.
Washington considers Yemen's al-Qaida in the Arabian Peninsula as the world's most dangerous branch of the terror network. In addition to drone strikes, the U.S. is supporting the government's fight against the group by providing help with logistics and military advisers.
Concerns over security at American embassies in the region are increasing after last month's deadly attack by militants against a U.S. diplomatic mission in Benghazi that killed the U.S ambassador to Libya and three other Americans. Protesters also stormed several U.S. embassies in Arab nations—including the one in Sanaa—in outrage over a film denigrating Islam's Prophet Muhammad.
Al-Qaida has called for more attacks on U.S. embassies and praised the killing of the ambassador.