"It is a possibility. No team should think they can escape at this level," Cookson told the French Le Monde newspaper.
The move comes after the introduction of a new World Anti-Doping Agency (WADA) code of conduct earlier this year, which allows tests on athletes at any time. However, legal wrangling over the terms used in the new code could mean that night raids are against French law. A government decree is expected to clarify the matter, but this is unlikely to be passed under after the Tour finishes.
Cookson also commented on Astana's controversial decision to let Lars Boom start the Tour de France after medical tests revealed that the rider had low levels of cortisol in his system.
Under the rules of the Movement for Credible Cycling (MPCC), of which Astana was a member, Boom should have been prevented from racing for seven days. However, Astana chose to let him start the Tour after they were denied the chance to substitute Boom.
Cookson said that Boom "broke no rules of the UCI or WADA", and highlighted the voluntary nature of the MPCC.