Kammala jumla mai zuwa: Kovalyov ya kasance mai sukar ra'ayi game da ra'ayoyin masu iko a cikin gwamnatocin Boris Yeltsin da Vladimir Putin. A cikin 1996, ya yi murabus a matsayin shugaban kwamitin kare hakkin dan adam na Yeltsin, bayan da ya wallafa wata wasika ga Yeltsin, inda Kovalyov ya zargi shugaban kasa da yin watsi da ka'idodin dimokiradiyya. A shekara ta 2002, ya shirya kwamiti na jama'a don bincika
1999 fashewar bama-bamai na Moscow (Hukumar Kovalyov), wanda aka gurgunta bayan da aka kashe daya daga cikin mambobinta, Sergei Yushenkov, wani memba, Yuri Shchekochikhin, wanda ake zargin an yi masa guba da thallium, kuma an kama lauyanta da mai binciken, Mikhail Trepashkin.