Kompany has been sidelined with a groin problem for the past few weeks and has missed several important games for his club, as well as being forced to pull out of Belgium's final two World Cup qualifiers last month.
Belgium have made it through to next summer's tournament in Brazil and will step up their preparations with a couple of friendlies, but Wilmots has resisted the temptation to call on Kompany.
City have clashed with the Belgian FA over Kompany in the past and former boss Roberto Mancini was critical of their decision to select him for a qualifier against Macedonia last season when he had just recovered from injury.
There will be no club versus country row on this occasion and Wilmots instead wants to help City get to the bottom of Kompany's fitness issues.
It is thought that the 27-year-old, who has not played for City since the win over Everton, could be fit to return to action against Tottenham Hotspur after the international break.
"Our physio, Lieven Maesschalck, will travel to Manchester on Friday to discuss the rehab programme with City's doctors and Vincent," Wilmots.
"We only play two friendlies, so it's good for him to have a good rest and that he recovers well to be on top with City again."
Kompany may be absent but there will still be a host of Premier League players in the Belgium squad for the games against Colombia on 14th November and Japan five days later.
The likes of Eden Hazard, Kevin de Bruyne, Simon Mignolet, Jan Vertonghen, Nacer Chadli, Mousa Dembele, Thomas Vermaelen, Christian Benteke, Kevin Mirallas, Marouane Fellaini, Nacer Chadli Romelu Lukaku are all set to join up with the national squad on Monday.
Manchester United's Adnan Januzaj has yet to pledge his international allegiance to anyone after previously rejecting a call-up by Belgium.
Wilmots has not heard of any fresh developments on the youngster's international future, adding: "He wants to focus on his career at United first.
"That is okay for me. Nothing has changed since then. There's no problem between us, I have respect for his choice."