RIA Novosti news agency said the cause of the fire is, instead, not known even though drones had been seen in the area, a flying device used by both sides.
In a press statement to Russian media outlet RBC, the company said the fire was the result of an "external influence". It also said it had paused operations at the port.
Yuriy Zapalatskiy, the head of Russia's Kingisepp district where the port is based, said in a statement there were no casualties, but the district has been placed on high alert.
News outlet Fontanka reported two drones had been detected flying towards St Petersburg on Sunday morning, but they were redirected towards the Kingisepp area.
The Russian Ministry of Defence did not report any drone activity in the Kingisepp area in its daily briefing. It said four Ukrainian drones had been downed in Russia's Smolensk region, and two more had been shot down in the Oryol and Tula regions.
Russian officials previously confirmed a Ukrainian drone had been downed on the outskirts of St Petersburg on Thursday.
Also on Sunday morning, at least 25 people were killed by shelling at a market on the outskirts of the city of Donetsk in Russian-occupied Ukraine, local officials said.
A further 20 people including two children were injured in the strike on Sunday morning in the suburb of Tekstilshchik, they said.
One local official said the shells had been fired by the Ukrainian military. Kyiv has not commented on the event and the claims could not be independently verified.