Here is the solution that works for me.
FactoryGirl.define do
factory :company do
#company attributes
end
factory :user do
companies {[FactoryGirl.create(:company)]}
#user attributes
end
end
if you will need specific company you can use factory this way
company = FactoryGirl.create(:company, #{company attributes})
user = FactoryGirl.create(:user, :companies => [company])
Hope this will be helpful for somebody.