Is it permissible to say Qunut (supplication recited while standing after bowing in the last unit of Prayer) in Fajr (Morning) Prayer and in Witr (Prayer with an odd number of units) Prayers
It is recommended to say the Qunut supplication in Witr Prayer, for
Al-Hasan ibn `Aly (may Allah be pleased with them) said,
The Messenger of Allah (peace be upon him) taught me some words to say during the Qunut supplication of the Witr Prayer; they were: "O Allah! Make me among those whom You have guided. Make me among those whom You have pardoned, and make me among those to whom You are a Patron, and bless that which You have bestowed on me and shield me against the evil of what You have decreed. Verily, You are the one who decrees and none can decree over You. He who You show allegiance to can never be abased, You are the Blessed and Exalted."
(Part No. 7; Page No. 46)
(Related by the Five Compilers of Hadith; Imams Ahmad, Abu Dawud, Al-Tirmidhy, Al-Nasa'y and Ibn Majah)
As for saying Qunut in the Fajr Prayer or in the other five obligatory prayers, it is not permissible. In fact it is a Bid`ah (innovation in religion) except if the Muslims face afflictions such as enemy attacks, deluges, plagues, etc. In that case it will be permissible to make Qunut asking Allah to remove it. The Messenger of Allah (peace be upon him) did so when some tribes killed some of his Sahabah (Companions, may Allah be pleased with them). Furthermore, he (peace be upon him) said Qunut in the Fajr Prayer after rising from Ruku` (bowing) in the second Rak`ah (unit of prayer). However, saying Qunut regularly in the Fajr Prayer is a Bid`ah. Although some scholars approved of it, it is not mentioned that the Prophet (peace be upon him) did so except in some weak Hadith.
Ahmad and the compilers of the Sunan related with a good Sanad (chain of narrators)
Sa`d ibn Tariq Al-Ashja`y who said, “I asked my father:
'You prayed behind the Messenger of Allah (peace be upon him),
`Aly; did they say Qunut in the Fajr Prayer?' He replied, 'Dear son! This is an innovation.'"
May Allah grant us success. May peace and blessings be upon our Prophet Muhammad, his family, and Companions.