Iryna Gerashchenko, who oversees humanitarian issues at truce talks periodically held in the Belarussian capital Minsk, said Russia's FSB security service informed her that she represented a national security threat.
"They told me that I am forbidden from entering the territory of the Russian Federation because I represent a threat to its territorial integrity, Russian defence capabilities and the health of its citizens," Gerashchenko wrote on Facebook.
Ukraine sent several deputies and President Petro Poroshenko's spokesman to the southern Russian city of Donetsk, where a judge was reading the verdict against Savchenko over the killing of two Russian journalists in war-torn east Ukraine in June 2014.
There was no immediate rection to Gerashchenko's statement from Russia, but the Ukrainian foreign ministry said it "expresses (its) strong protest".
"By not allowing Iryna Gerashchenko to attend the court hearing of this fabricated case against Nadiya Savchenko, the Russian authorities intentionally created an artificial barrier to the Ukrainian representative's... performance of her direct duties," the ministry said in a statement.
The Minsk talks, which are being coordinated by the Organization for Security and Co-operation in Europe (OSCE), are aimed at resolving issues standing in the way of ending Ukraine's 23-month separatist war, which has claimed nearly 9,200 lives.
Prosecutors have demanded 23 years in jail for Savchenko, a 34-year-old army helicopter pilot who was serving in a pro-Kiev volunteer battalion fighting pro-Russian rebels in east Ukraine at the time of the journalist deaths.
Savchenko has denied the charges and her trial has sparked widespread condemnation from both Ukraine and its Western allies.