Hutsol, 31, sought refuge in Switzerland last autumn after being beaten several times in Ukraine.
But her application for asylum was turned down by the Swiss Federal Office for Migration on technical grounds, 20 Minuten newspaper reported on Thursday.
Because Hutsol had previously stayed in France before coming to Switzerland, the office ruled that it is up to French authorities to consider her application as an asylum seeker.
She appealed the decision but without success, the Südostschweiz newspaper reported.
Hutsol had hoped she would be able to stay because she has a sister living in Winterthur in the canton of Zurich.
The dissident is currently staying at the Landegg asylum centre for refugees at Rorschacherberg, Saint Gallen.
In an interview with 20 Minuten earlier this month, Hutsol said she wanted to return to Ukraine as soon as possible but this is considered too dangerous at the moment.
Swiss authorities say she will be transported to France at the earliest opportunity.
Hutsol continues to be involved in planning Femen protest actions.
The group has expanded from Kiev to establish a base in Paris along with branches in at least seven other countries.
“It is quite clear that you will see us again,” Hutsol told 20 Minuten.