The cyclist, 24, has been using the compound since 2011, but which was only banned from the beginning of the year.
The Estonian Cyclists Union said Pruus did not know about renewing of the banned substances list and has admitted to taking the drug, which is still allowed during non-competing periods.
Pruus had not been banned from competing, but has voluntarily dropped out of future competitions until the matter is resolved. An international disciplinary committee has been summoned, which could issue a warning instead of a ban.
Trimetazidine usually prescribed as a long-term treatment of angina of the heart, and in some countries for tinnitus and dizziness. It is commonly used to improve valve function in diabetic patients with coronary heart disease.
Pruus, who rides with the Rietumu-Delfin team, placed fifth in the Estonian national championships on June 27 and 12th in the Estonian road race championships on June 29th.