Guwahati franchise co-owner John Abraham had announced the name of the team as North East United FC on June 10.
"The Assam government has spent more than Rs 12 crore in refurbishment of the infrastructure in Guwahati so that the ISL team can be based in the city. So, Guwahati's name should have been reflected in the name of the club," Dutta said.
"I have no problems with John Abraham's idea of the team being projected to represent the entire North East region. But with Assam government spending tax-payers money for the benefit of the team, then I feel it is also necessary to reflect Guwahati in the name of the team," he added.
Dutta, who is also an Executive Committee member of All India Football Federation and vice-chairman of I-League Committee, said that he would write to the ISL organisers IMG-Reliance on this issue.
"The names of two teams of ISL have been announced. In both the teams, Kerala Blaster FC and Atletico de Kolkata the name of the home city or the state is being mentioned. Then why not in the case of Guwahati franchise," said Dutta.
"When tender for franchises was floated by IMG-Reliance, it said Guwahati franchise or Kolkata or Kochi franchise. Then, why was the name of Guwahati franchise made North East United FC?" Dutta asked.
"I am going to write to IMG-Reliance on this issue," he added.
I-League side Shillong Lajong FC owner Larsing Ming Sawyan is the other co-owner of the Guwahati-based ISL team.
The inaugural season of the ISL is scheduled to run from September to November this year.
When contacted, Shillong Lajong officials refused to comment on the issue.