Reciting Qunoot-e-Nazilah is an absolutely authentic practice. If a calamity (Nazilah) befalls the Muslims, it is prescribed to say Dua al-Qunoot after standing up from Rukoo in the last Rakah of each Salah, until Allah (swt) relieves the Muslims of that calamity.
In fact, this Sunnah is still practiced in many of the Arab countries.
With regard to saying Dua al-Qunoot in Fajr prayer all the time in all circumstances, there is no Saheeh report that the Prophet (sa) singled out for Fajr for reciting Dua al-Qunoot all the time or that he always recited in Fajr prayer.
Rather, what is proven is that the Prophet (sa) used to say Qunoot at times of calamity only, with words that were appropriate to the situations. This can be done in any of the five obligatory prayers.
It is proven that the Prophet (sa) used to say Qunoot at times of calamity, praying against the aggressors among the disbelievers and praying for the weak and oppressed Muslims to be saved from the plots and captivity of the Kafirs.
The Prophet (sa) offered supplication (Dua) at times of calamity on a number of occasions, and his supplication was appropriate to the calamity, for which he was praying Qunoot.
He (sa) prayed against some of the Arab tribes, who had betrayed 70 of the Sahabah and killed them – he prayed that they be cursed. It was narrated that Ibn Abbas said:
“The Messenger of Allah (sa) prayed Qunoot for a month in Zuhur, Asr, Maghrib, Isha and Fajr prayers, when he said “Sami’Allahu Liman Hamidah” in the last Rakah, praying against the last tribes of Banu Sulayman and against Ri’l, Dhakwan and Usayyah, and those, who were beside him, said “ameen”. (Abu Dawood)
According to a report narrated by Muslim, he said: “O Allah curse Banu Lihyan, Ri’l, Dhakwan and Usayyah, for they have disobeyed Allah and His Messenger.”
According to a report narrated by Bukhari (4070) from Ibn Umar (rtam), he (Ibn Umar) heard the Messenger of Allah (sa) say, when he lifted his head from bowing in the second Rakah of Fajr: “O Allah, curse so- and-so, and so-and-so, and so-and-so,” after he said “Sami’ Allahu Liman Hamidah, Rabbana Wa Laka’l Hamd.”
Rightly guided Khaleefahs after him followed the same practice. It is better for the Iman to limit Qunoot-e-Nazilah to times of calamity only.
Allah (swt) knows best.
What are the words of Qunoot-e-Nazilah?
The correct view, which is of majority of scholars, is that there are no specific words with regards to what is to be said in Qunoot-e-Nazilah. Rather, any Dua may be said, depending upon the situation and requirement.
When praying Qunoot at the time of calamity, one should make supplication, which is appropriate to the situation, as it was narrated that the Prophet (sa) cursed some Arab tribes, who had betrayed his companions and killed them, and he prayed for the weak and oppressed believers in Makkah that Allah (swt) would save them.
It was narrated that Umar (rtam) prayed Qunoot with the following words:
اللَّهُمَّ اغْفِرْ لَنَا وَلِلْمُؤْمِنِينَ وَالْمُؤْمِنَاتِ وَالْمُسْلِمِينَ وَالْمُسْلِمَاتِ وَأَلِّفْ بَيْنَ قُلُوبِهِمْ وَأَصْلِحْ ذَاتَ بَيْنِهِمْ وَانْصُرْهُمْ عَلَى عَدُوِّكَ وَعَدُوِّهِمْ اللَّهُمَّ الْعَنْ كَفَرَةَ أَهْلِ الْكِتَابِ الَّذِينَ يَصُدُّونَ عَنْ سَبِيلِكَ وَيُكَذِّبُونَ رُسُلَكَ وَيُقَاتِلُونَ أَوْلِيَاءَكِ اللَّهُمَّ خَالِفْ بَيْنَ كَلِمَتِهِمْ وَزَلْزِلْ أَقْدَامَهُمْ وَأَنْزِلْ بِهِمْ بَأْسَكَ الَّذِي لا تَرُدُّهُ عَنِ الْقَوْمِ الْمُجْرِمِينَ بِسْمِ اللَّهِ الرَّحْمَنِ الرَّحِيمِ اللَّهُمَّ إِنَّا نَسْتَعِينُكَ وَنَسْتَغْفِرُكَ وَنُثْنِي عَلَيْكَ وَلا نَكْفُرُكَ وَنَخْلَعُ وَنَتْرُكُ مَنْ يَفْجُرُكَ بِسْمِ اللَّهِ الرَّحْمَنِ الرَّحِيمِ اللَّهُمَّ إِيَّاكَ نَعْبُدُ وَلَكَ نُصَلِّي وَنَسْجُدُ وَلَكَ نَسْعَى وَنَحْفِدُ وَنَخْشَى عَذَابَكَ الْجِدَّ وَنَرْجُو رَحْمَتِكَ إِنَّ عَذَابَكَ بِالْكَافِرِينَ مُلْحِقٌ
O Allah, forgive the believing men and believing women and the Muslim men and Muslim women, bring their hearts together and reconcile between them, support them against Your enemies and their enemies. O Allah, the curse is upon those who disbelieved among the people of the Scripture, who obstruct people from Your path and have denied Your Messenger and have fought Your allies. O Allah, oppose their words and shake their footing and send upon them Your strength which the criminals cannot repel. In the name of Allah, the Gracious, the Merciful, we seek Your help and we seek Your forgiveness. We praise You, we do not deny You, and we disavow and abandon whoever is wicked to You. In the name of Allah, the Gracious, the Merciful, You alone we worship, we pray to You, we prostrate for You, we strive for You, we fear Your punishment and we hope in Your mercy. Verily, Your punishment of the unbelievers will be carried out.”
Source: as-Sunan al-Kubra lil-Bayhaqī 3143; Grade: Sahih (authentic) according to Ibn Hajar
(Hadith wording taken from this website)