The two 16-year-olds and a third man aged 19 disappeared on Thursday night in the West Bank, where they were seminary students in a Jewish settlement.
"These teenagers were kidnapped and the kidnapping was carried out by Hamas members," said Prime Minister Benjamin Netanyahu, referring to the Palestinian Islamist group that controls the Gaza Strip.
There has been no public claim of responsibility. Asked about Netanyahu's allegations, Sami Abu Zuhri, a Hamas spokesman in the Gaza Strip, stopped short of a clear denial or confirmation that it was involved.
Since the three went missing, apparently while hitchhiking, the Israeli army has carried out house-to-house searches, round-ups and interrogations in the Palestinian city of Hebron and outlying villages.
The military said as part of the "effort to return the three abducted Israeli teenagers approximately 80 Palestinian suspects were detained in a widespread overnight operation".