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Kondogbia's failure to turn up prompted the 24-year-old to be axed from Inter's squad for Saturday's friendly against Real Betis.
A furious Spalletti told reporters he had been unaware of the defensive midfielder's desire to change teams.
"He (Kondogbia) had this idea to change, it came out of the blue and I tried to convince him (to stay), but someone else probably made certain promises," Spalletti was quoted as saying in Italian daily Gazzetta dello Sport.
Spanish club Valencia are reported to be interested in the player but Inter are refusing to sell for less than 25 million euros ($29 million).
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Spalletti stressed however that "Kondogbia is an important player" in their quest for a first Serie A title since 2010.
Kondogbia joined the Milan giants in 2015 from Monaco having previously spent a season in Spain at Sevilla.