Lisin was assigned to the San Antonio Rampage on Monday. Instead, he returned to Russia where he is expected to play for Ak Bars Kazan of the Russian league.
"We are very disappointed in Enver's decision to not report to the San Antonio Rampage," general manager Michael Barnett said in a statement. "We fully expected him to honour his contract, thus we have no choice but to suspend him as a result of his actions."
Lisin, 20, registered a goal and an assist with 16 penalty minutes in 17 games with the Coyotes this season.
But the Russian, who scored his first NHL goal on Nov. 4 against Los Angeles, had trouble playing defence and was a minus-18.
"He has the tools to one day be an NHL player, but his defensive liabilities negated him from playing regularly at the NHL level at this time," Barnett said. "The AHL would have been an ideal situation for him to learn the North American pro game on the smaller ice surface.
"We waited two full years after drafting him before bringing him over. We were conscious of not wanting to rush him. It's not always easy for young players from those countries to adapt to life in America ... particularly if it calls for time in the minors. But going there and learning the game is part of being a pro and paying the price."
A similar situation happened earlier this month, when the Ottawa Senators suspended centre Alexei Kaigorodov Nov. 4 for refusing to accept his AHL assignment.
Lisin was recalled by the Coyotes from San Antonio on Oct. 12 and made his NHL debut on Oct. 14 against Nashville.
In two games with San Antonio this season, the six-foot-two, 190-pound forward scored two goals.
The Coyotes selected Lisin in the second round (50th overall) of the 2004 draft.