Speculation has mounted that the Italian's position with the Nerazzurri is growing ever more tenuous after the club lost further ground in the race for a Champions League berth in the 2-2 draw with Bologna on Saturday.
Former boss Roberto Mancini is among those linked with taking charge of the Serie A giants in the summer, but Thohir insists that Mazzarri will be in charge for the 2014-15 campaign.
"We have no problem," the Indonesian told Sky Sport Italia.
"The professional relationship with Mazzarri will continue next season. We will start to work out some new targets in the market as it is very important to prepare."
Inter face an away trip to Sampdoria next Sunday.