Skvernelis said that the Tibetan spiritual leader's representatives had not expressed such a wish either.
"We coordinate positions and meet when there is a need from one side or the other. There was no such need, and hence there was no such meeting," he told reporters on Wednesday.
The Dalai Lama, who arrived in Lithuania on Tuesday, is scheduled to meet on Thursday with Tibetan supporters in Lithuania, including some politicians, business people and public figures. The country's top officials will not be present either in person or be represented in the meeting.
Beijing warned ahead of the Dalai Lama's visit that it might harm bilateral relations.
Skvernelis says that the Tibetan spiritual leader's visit should not damage Vilnius' relations with Beijing.
"(These relations) are really good, growing, dynamic," he said.
This is the Dalai Lama's fourth visit to Lithuania.
President Dalia Grybauskaitė met with the Tibetan spiritual leader during his visit back in 2013, which caused a cooling of bilateral relations for several years.