Several medical facilities with links to the UN have been destroyed by bombs. (Representational)

Russia on Monday denied a US newspaper report that its warplanes bombed four hospitals in rebel-held territory in Syria over a period of 12 hours this year.

The Russian defence ministry rubbished the claim in a report by The New York Times, saying "the alleged 'evidence' provided by the NYT is not worth even the paper it was printed on".

The May strikes -- which the newspaper tied to Moscow through Russian radio recordings, plane spotter logs and accounts by witnesses -- are part of a larger pattern of medical facilities targeted by forces supporting Syrian President Bashar al-Assad in the country's devastating civil war.

Nabad al Hayat Surgical Hospital -- which staff had fled three days earlier in anticipation of the facility being bombed -- was one of those struck during the 12-hour period beginning on May 5, according to the Times' investigation.

A Russian ground controller gave the exact coordinates of the hospital to the pilot, who reported having it insight a few minutes later, the newspaper said.

The controller gave the go-ahead for the strike at the same time that a spotter who was tasked with warning civilians about impending strikes logged a Russian jet in the area.

The pilot then reported releasing bombs, and local journalists filming the hospital recorded three bombs going through its roof and exploding.

Kafr Nabl Surgical Hospital -- just a few miles (kilometers) away -- was bombed multiple times shortly afterwards.

As with the earlier strike, a spotter registered one of Moscow's jets circling, and a Russian air force transmission recorded a pilot saying he had "worked" the target before delivering three strikes that were confirmed by a doctor, the Times said.

The Kafr Zita Cave Hospital and Al Amal Orthopedic Hospital were also bombed by Russian aircraft during the 12-hour period. All four facilities had provided their coordinates to the United Nations for inclusion on a list to avoid strikes.

Russian defence ministry spokesman Igor Konashenkov in a lengthy statement reacting to the report claimed The New York Times had become a "victim of manipulation by terrorists and British security services".

He took issue with a number of details in the report including the anonymity of the newspaper's sources and said that radioed voice commands are not used to pass coordinates to pilots of Russian fighter planes in Syria.

UN Secretary-General Antonio Guterres announced last month that he was setting up an internal investigation into the bombing of hospitals in Syria that had previously flagged their coordinates.

Several dozen medical facilities with links to the UN have been damaged or destroyed by bombs this year. Russian has denied deliberately targeting civilian installations.