Malik, 22, who quit the popular boy band in March 2015, asked Tomlinson to "stop making bitchy comments" when the singer poked fun at a picture of the musician with his new friend Naughty Boy.
Tomlinson, 23, during his recent appearance with other 1D members on James Corden's show, however said the duo were "on good terms," reported Aceshowbiz.
"We are on good terms. It has all been resolved, I have never have been good at holding my tongue I think I get it from me mum," Tomlinson said.
As the topic switched to Malik's departure from the pop group in March during the band's world tour, Tomlinson said that all the band members "were angry but it's better now".
"There were parts of this job that Zayn loved, but there were parts he hated. And you can't hate this job at all, or only like some of it. So he had to do what was best for him. We wish him the best of luck... No hard feelings," he said.