The "90 Day Fiance" star tells TMZ ... he's aware he and his 3-year-old have officially been reported as MIA in Louisville, KY -- made public in a since-deleted bulletin posted by Missing People in America -- but denies he's kidnapped and fled with his own kid ... saying they were simply on a long work trip together dating back to early June, and that Pierre is safe.

Paul -- who says he's had, in recent months, sole custody of his 2 children, Pierre and Ethan, whom he shares with ex-wife, Karine Martins -- explains that he's been bouncing around these past few weeks between Pennsylvania and FL with Pierre, as PS seeks work.

The reason he brought Pierre with him for this journey, he says, is because the kid suffers from extreme separation anxiety. Since they left, though, local CPS officials have taken custody of his other son (who was staying with Paul's mom, we're told) ... and then filed a missing person's report with cops. Louisville Metro PD confirms to TMZ they took the report.

As for what's going to happen now ... Paul tells us he and Pierre are heading back to Louisville STAT to deal with this mess, and he hopes to regain custody of his children on his own or through his folks by going to court, which he says he'll do in the coming weeks.

As for why he's even dealing with custody issues in the first place ... well, '90 Day' fans are probably well aware of his and Karine's tumultuous relationship dating back to the 2010s -- when they were on the show -- which has only gotten more volatile after tying the knot.

The most recent hiccup between them went down last year, when video purportedly showed Karine being abusive to Paul ... on the heels of a reported divorce filing. Unclear where things stand now, but it appears the powers that be have stepped in over their kids -- who are alleged to have been present during some of the dust-ups between the parents.