Zimbabwe and Nepal were suspended in July this year following government interference in the running of the Board.
The Zimbabwe cricket board has been reinstated by a government body but the country remains suspended by the International Cricket Council because of outside interference.
Flower said Sports and Recreation Committee is a public body and he didn't seem to agree with the way the ICC has interpreted government intervention in this case.
If Zimbabwe don't end up participating, the series is likely to be turned into a bilateral affair.
The ICC on Thursday suspended Zimbabwe Cricket for violating its constitution, a decision which evoked sympathy for the country's affected cricketers.
Sources at the ZC claimed that reinstating the elected body would be difficult by October.
India are scheduled to play three T20Is against Zimbabwe in Guwahati on January 5, Indore on January 7 and Pune on January 10.
On Thursday, the ICC suspended Zimbabwe Cricket with immediate effect in violation of the global body's constitution.
The ICC on July 18 suspended Zimbabwe Cricket with immediate effect for failing to fulfil their obligation of ensuring that there is no government interference in its administration.
Political turmoil within the sport and a string of humiliating performances led Zimbabwe to suspend their involvement in Test cricket in 2005.
Ntini, 40, who played 101 Tests for the Proteas, has held the responsibility of bowling coach since January 2016 for a term of two years.