UPDATE 1-Japan's JX shuts desulphurisation unit after fire

* Fire hit Kashima refinery's unit twice but extinguished

* No injuries

* Cause uncertain; no impact to other refining units (Adds details)

TOKYO, Oct 2 (Reuters) - Japan's top refiner, JX Nippon Oil & Energy Corp, a unit of JX Holdings , said it conducted an emergency shutdown of the 30,000 barrels per day No.1 fuel oil desulphurisation unit at Kashima refinery, northeast of Tokyo, on Saturday due to a fire, but added that other refining units continued operations.

The fire occurred around the unit's tower facility at about 3:30 p.m. (0630 GMT) on Saturday and was extinguished by about 9 p.m. (1200 GMT).

But the unit again caught fire at 10:54 p.m. (1354 GMT) in the same place, and the fire was extinguished by 0:30 a.m. on Sunday (1530 GMT on Saturday), the company said in a statement. There were no injuries.

Other units at the refinery, including the 189,000 bpd crude distillation unit (CDU) and the 63,500 bpd condensate splitter, have continued operations following the fire, but the run rate has fallen, an official at the refinery said, without giving more specifics.

The 252,500 bpd Kashima refinery, hit by a magnitude 9.0 quake in March, resumed refining operations in June, but the run rate had been kept low at around two-thirds of capacity because Very Large Crude Carriers (VLCC) could not be docked until late last month due to damage to berthing facilities.

But as the repair to berths neared completion, a VLCC docked at the refinery on Sept. 24, the first time since the March quake, and the firm had begun raising crude runs, with aims to resume full-capacity operations from mid-October, when the fire occurred, the refinery official said.

The official added that it has been continuing to cool the unit to avoid a third fire from breaking out. The cause of the fire was unknown, but it will be investigated, the official added. (Reporting by Osamu Tsukimori; Editing by Michael Watson)