The coach admits the club's board may force his hand as the Stamford Bridge outfit eye a move for the midfielder, who has also attracted interest from Manchester United
Goal reported in December that Chelsea had stolen ahead of Manchester United in the race for the Colombian, and talks with the Blues have since been confirmed by the player's agent and club.
Mazzarri is eager to keep him at the Giuseppe Meazza, but he admits the club could opt to cash in on the 27-year-old.
"Clearly I'd like him to stay, but if his sale is being considered then that explains the club's situation," he told RAI Sport. "This year there are eight players coming towards the end of their contracts."
Inter were beaten 1-0 by Udinese in the Coppa Italia on Thursday and Mazzarri was left fuming after Diego Milito - making his first start for the Nerazzurri in a year - was denied a penalty for a clear shirt-pull.
"The second half was an Inter monologue," he continued.
"It's becoming a joke now. You too saw the incidents today, so nobody can say: 'Mazzarri complains about referees.' I don't want to talk about it any more for the rest of the season.
"We are a work in progress and I had to evaluate a few things, so I needed this game to experiment. We were a little shaken up in the first half and suffered due to Udinese's pressing. The result is harsh on us, but these things happen in football.
"Milito's comeback is important, as he hadn't played 90 minutes in a year. Now we must concentrate on Serie A with a player like Milito back in our ranks."
Inter's last-16 defeat is their first at that stage since 2002 and follows a disappointing Serie A loss to Lazio, but Mazzarri maintains the club is on track as he looks to restore them as a major force in Italian football.
"This summer we set certain parameters and we're on track with those. We're missing a few points in the league, but I think we are doing very well," he added.
"I don't have to convince anyone, as last season Inter failed to qualify for Europe for the first time in 14 years and it's a sign this club is going through a difficult time.
"People must accept we are a work in progress. We've only lost three games and had a few too many draws, but this squad has a soul and cannot do everything in one year."