I am going to do B.Sc Agriculture from a college which is not certified by ICAR, will I face any problem in getting a government job?

You are eligible for writing government exams like SSC CGL UPSC SBI and other government-related exams, but I don't think there is a need of studying agriculture for those jobs, a normal degree is enough for writing those exams. Moreover, the eligibility varies from state to state, do some research

No, it is not necessary that every institute is accredited by ICAR. Make yourself enough skillful and you will get decent chances to get government jobs. All the best.