"Deeply pained by the attacks in Egypt. We condemn these attacks. My thoughts are with families of the deceased & prayers with the injured," PM Modi tweeted.
The first explosion, which left 27 dead and 78 injured, ripped through a Palm Sunday service at Mar Girgis (St. George's) Coptic church in Tanta, a city located 120 km from Cairo, EFE news reported.
The explosive device was planted under a seat in the church and was detonated in the main prayer hall.
A short while later, a suicide bomb attack outside Saint Mark's Coptic Orthodox Cathedral in Alexandria killed 17 and injured 41 people, according to a Health Ministry statement.
"This is an impious terrorist act, but we will eradicate terrorism from Egypt and we are determined to put an end to terrorist groups," EFE news quoted Ismail as saying.
Copts, who make up around 15 per cent of Egypt's population, were celebrating Palm Sunday, which marks the start of the Holy Week for Christians.
This attack comes just 20 days before the visit of Pope Francis, who is set to travel to Egypt on April 28.