Finnish police in late October recovered an anchor believed to have damaged the Balticconnector pipeline between Finland and Estonia on October 8.
They said findings suggested it belonged to the Chinese cargo ship Newnew Polar Bear.
"The presidents noted the constructive dialogue between the countries regarding the Balticconnector pipeline incident," a statement from the Finnish presidency said.
A Chinese statement about the presidents' video-link meeting made no mention of talks on the damaged pipeline.
Finnish officials said in late October that China was cooperating in its investigation.
The incident came just over a year after underwater explosions struck three of four Nord Stream gas pipelines in the Baltic Sea, cutting off a major supply route to Europe from Russia at a time of heightened tensions between Moscow and the West over the war in Ukraine.
The cause of that sabotage remains unknown.
The Finnish operator of Balticconnector said in October it would take at least five months to repair the pipeline, leaving Finland dependent on liquefied natural gas imports for the winter.
Natural gas accounts for around five percent of Finland's energy consumption, being mainly used in industry and combined heat and power production.
In the Finnish statement, Niinisto, whose country joined NATO last year, said he had also raised the issue of the war in Ukraine in his talks with Xi and "stressed the role of China in achieving a just and lasting peace."
In a summary of the meeting on Chinese state television CCTV, Xi said the Asian nation was "firmly pursuing an independent foreign policy of peace."
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