The 61-year-old momager split from Caitlyn Jenner, 67 - who was known as Bruce before her gender transition - in 2013 and although they initially remained friendly, they fell out after Caitlyn blasted Kris in her recent memoir.
A source told PEOPLE: ''Kris is not thrilled [that the girls spend Father's Day with Caitlyn]. It's a very complicated situation for the girls. Kendall and Kylie just won't speak with Kris about it. Caitlyn is their dad, but they also don't want Kris to be upset so they just won't talk about it.''
It was recently claimed that Kendall, 21 and 19-year-old Kylie were struggling to cope with the tension between their parents.
Kylie has reportedly tried to ''not take sides'' during the ongoing drama as she still wants to ''have a relationship'' with Caitlyn, but insiders claim the whole ordeal has made it ''very difficult'' for her to do so.
A source said: ''Kylie has really made an effort not to take sides and to be supportive of Caitlyn. She really wants to have a relationship with her dad, but Caitlyn has hurt Kris tremendously and it's made it very difficult. With everyone in the family on Kris' side, it's hard on Kylie. She tries to keep it separate and doesn't want to discuss it with the rest of the family.''
And Kendall reportedly has had a ''very strained'' relationship with the 'I Am Cait' star.
The source told E! News: ''[Their relationship is] very strained. [Kendall] rarely speaks to Caitlyn. Kendall is loyal to Kris and has very little to do with her dad. The more time that has passed, the more she feels Caitlyn has let her down with the things she has said and with her actions.''
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