Earlier the Palestinian Ma'an news agency claimed a military reconnaissance plane was flying over the area and checkpoints had been erected.
Israeli military sources later acknowledged the reported search, after media in the country were earlier banned from publishing any details.
It is thought an Israeli car was earlier found on fire and that the incident could be linked to the disappearance.
Ma'an said eyewitnesses had reported Israeli forces searching the car, removing items and moving local Palestinians away from the area.
The teenagers are thought to have initially contacted the IDF by phone, but the line of communication was later lost.
