It was escorted by Border Security Force (BSF) and state police personnel.
The arrival of the two teams from Delhi without prior information on Monday had triggered a tussle between the Centre and the state government.
While one team is in the city, another one is in Jalpaiguri district.
They have been sent to take stock of the COVID-19 situation in Kolkata and some other parts of the state.
In addition to West Bengal, inter-ministerial teams of the Union government have also been sent to Madhya Pradesh, Maharashtra and Rajasthan for an on-the-spot assessment of the situation arising out of the coronavirus pandemic in these states.
The central team was seen coming out of the BSF office in south Kolkata at around 4.45 pm. It then visited certain areas of the city.
Apurva Chandra, the leader of the team who had claimed in the morning that they were told they "will not be going out" during the day, was seen sitting in one of the cars.
Earlier in the day, talking to a news channel, Chandra, an additional secretary in the defence ministry, said, "We have been deployed by the Centre and our order of deployment says the state government shall provide logistic support to us.... I have been in touch with the chief secretary and seeking his support since the time I landed here.
"I met him on Monday. But on Tuesday, we were informed that there were some issues, so we will not be going out. The chief secretary is likely to visit us and we will again hold a meeting with him."
He said they had made it clear that they would be accompanied by state government officers in order to make their visit more productive.
"But now, it has been more than a day and we have only visited the NICED (an ICMR facility) and the state secretariat," Chandra said.
State Chief Secretary Rajiva Sinha said, "The central team told us that it wants to visit parts of the city. We agreed and state government officials are accompanying the team." PNT SNS RC