Royal Marines joined the rescue effort today but hopes were fading for the boys, who disappeared last night at the Lulworth Cove beauty spot in Dorset.
A 15-year-old boy raised the alarm after seeing his two friends, aged 15 and 16, disappear into the water as force nine gale battered the south coast of England.
A spokesman for Dorset Ambulance said: "We treated the 15-year-old at the scene for a hand injury. We hear he had grabbed hold of a buoy before swimming back to shore."
Mark Rodaway, Coastguard commander for southern England, said it was still not clear what the boys were doing in the area.
He said: "We understand that they were either engaged in fishing or they were watching some fairly spectacular seas coming in the Cove area. It was just after that when the boys were swept into the water and the alarm was raised just after 7.20 yesterday evening.
"They were a group of three friends - two were on a ledge slightly lower, one was on a ledge slightly above them. A large wave came in, swept two into the water and the third young person tried to effect a rescue, we understand.
"He entered the water to try and help his friends but couldn't see them because it was dark. After 7pm it's pitch dark and we have raging seas. He fortunately gained the shore and raised the alarm."
Mr Rodaway added: "Because of the sea conditions and the duration that we have been searching, a successful outcome is looking less likely. That doesn't mean to say we will stop searching because clearly we want to recover both boys to their families but the successful outcome is looking less likely."
He said the water temperature was 14C and a person could survive in such temperatures for around three hours without wearing survival equipment.
"What we are hopeful for at the moment is that the boys made the shore and that they are injured somewhere we can access them."
A spokesman for Weymouth Lifeboat said: "The Swanage lifeboat has gone back out and we understand the Royal Marines are sending some of their surf boats. There are three or four ground-based Coastguard teams searching the cliffs."
A Coastguard rescue helicopter and two Weymouth lifeboats began searching the area last night. The Lulworth and Kimmeridge Coastguard rescue teams were scouring the shoreline today.
Chief Inspector Nick Maton, of Dorset Police, said the boys were not thought to be related but were a group of three friends.
Mr Maton said the boy who raised the alarm was being interviewed by family liaison officers and added: "He is highly traumatised by all this."
The boys were playing on ledges at the bottom of the western tip of the cove. The only access is by scrambling along loose rocks where the sea and cliffs meet.
Warning signs at Lulworth Cove, a Unesco-designated World Heritage Site, state that climbing is prohibited and it is "extremely dangerous" to climb or sit beneath the cliffs.
Richard Holman, headteacher of The Purbeck School, confirmed that the two missing boys attended his school in Wareham, Dorset. He said that pupils in the same year as the two missing boys had been informed of the situation.
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