Mexican officials ordered a temporary occupation of the facility in December and in February declared the U-3400 unit at Pemex's Tula refinery in Hidalgo state a public good, preparing the way for its formal expropriation.
Oil refineries use hydrogen to reduce the sulfur content in petroleum products, especially diesel.
The decree calls on Pemex to compensate Air Liquide, but does not detail the amount.
Paris-based Air Liquide did not immediately respond to Reuters' request for comment.