New Delhi is suspicious of China's increasing presence in the Indian Ocean and its influence in Sri Lanka, which is strategically placed halfway along key east-west international shipping routes.
The 90-metre (300-foot) vessel was seen entering the port of Colombo on Wednesday afternoon.
A foreign ministry spokesman said the vessel had been authorised to dock in the city, where a Chinese state-owned company operates a deep-sea container terminal.
"Clearance was given for the vessel to come to Colombo for replenishment," the spokesman, who asked not to be named, told AFP.
There was no immediate comment from either the Chinese or Indian diplomatic missions in Sri Lanka.
Chinese state broadcaster CGTN calls the Shi Yan 6 a "scientific research vessel" with a crew of 60 to conduct oceanography, geology and marine ecology tests.
The foreign ministry did not say how long the vessel would remain docked in Colombo.
Last year, India expressed concerns over a similar port call by Chinese research vessel Yuan Wang 5, which specialises in spacecraft tracking and which New Delhi described as a spy ship.
It docked in Hambantota, a port in Sri Lanka's south under a 99-year lease to the Chinese company that built it after Colombo was unable to service a $1.4 billion loan taken for the project.
Sri Lanka defaulted on its $46 billion external debt last year in an unprecedented economic crisis partly blamed on Chinese loans used to build white-elephant infrastructure projects between 2005 and 2015.
China owns 52 percent of Sri Lanka's bilateral debt, and Beijing's approval is crucial for any efforts by Colombo to restructure its outstanding loans.
President Ranil Wickremesinghe attended a Beijing forum last week for China's multibillion-dollar Belt and Road Initiative global infrastructure programme.
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