Latvia's Dievturi congregation and Lithuania's Romuva community expressed respect for the pope in a joint message.
But they said that some in the Catholic hierarchy have been blocking their bid for the official status of a religion.
“We sincerely hope that, while you visit, You will urge the brothers and sisters of Your religious beliefs to respect our own religious choice and cease impeding our efforts to achieve national recognition of the ancient Baltic faith,” the groups said in a letter to the pope seen by AFP on Friday.
Ramunas Karbauskis, a farming tycoon and leader of Lithuania's governing Peasants and Green Union party, is widely regarded as having masterminded moves to accord Romuva legal status in the predominantly Catholic country.
The move would give pagan marriages and baptisms the same civil status as Christian, Jewish or Muslim ceremonies.
But the Lithuanian parliament has postponed examining the issue, a move some commentators attribute to the pope's visit.
The Romuva community numbers more than 5,000 followers, according to the 2011 census — more than the 3,000 Jews who enjoy legal status.
There are no equivalent statistics available for the Latvian pagan community.