Local residents said they had spotted China's Xiang Yang Hong 3 at the Thilafushi industrial port near the capital Male.
The 100-metre-long (328-foot) vessel was at an anchorage near Male on Thursday evening, according to the website Marinetraffic.
The Maldives' pro-Beijing government said earlier the vessel was docking for a port call to rotate crew and take on supplies, on the condition that it would not conduct "research" while in its territorial waters.
Media reports in India had suggested that the vessel was conducting surveillance for Beijing.
India is suspicious of China's increasing presence in the Indian Ocean and its influence in Sri Lanka and the Maldives, which are strategically placed halfway along key east-west international shipping routes.
Relations between Male and New Delhi have chilled since pro-China President Mohamed Muizzu won elections last year.
Muizzu has asked India to withdraw 89 security personnel based in the Maldives to operate reconnaissance aircraft by March 15.
But the president has also insisted he does not want to upend ties with New Delhi by replacing Indian troops with Chinese forces.
Sri Lanka refused entry to Xiang Yang Hong 3 after two other port calls from Chinese vessels since 2022 raised objections from India.
That included the ship Yuan Wang 5, which specialises in spacecraft tracking and which New Delhi described as a spy ship.
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