American magazine US Weekly claims Tom is allowed to visit his daughter for up to 10 days a month, but "chooses not to because she's not a Scientologist".
Tom, 56, divorced Suri's mum, Katie Holmes, in 2012 after six years of marriage.
The youngster went to live with her mum after the split, but Tom was granted visiting rights.
However, the magazine now reports that it's been "years" since Tom last saw his daughter and they haven't been pictured together since 2013.
Tom remains devoted to Scientology and reports suggest that Katie and Suri left the church after the divorce.
Scientology critic Tony Ortega told the publication that Tom's ex-wives – Katie and Nicole Kidman – lead very separate lives to the actor now.
He said: "Katie and Nicole have moved on from their time with Tom and are leading their own lives outside of the church."
Nicole also left the church after her split from Tom back in 2001, but their two adopted children, Connor and Isabella, stayed with their dad and were raised within the Scientology community.
The Oscar-winning actress went on to marry country star Keith Urban and have two daughters with him, but she's believed to remain estranged from Connor and Isabella.
Tom was introduced to Scientology by his first wife Mimi Rogers, who he divorced in 1990.
He's gone on to become one of the Church's most high-profile members.
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