"The applicant's appeal was rejected and the court recognized that the permit had been revoked on reasonable grounds as the available data suggests the applicant poses a threat to national security," Audris Kutrevicius, a spokesman for court, told BNS.
The public broadcaster LRT was the first to report the news.
The LRT Investigation Team reported earlier that Yelena Kaminskas (nee Shebunova), is an ex-girlfriend of Shoigu, with whom she shares two children. She is married to businessman Adolfas Kaminskas, who has double Lithuanian-Russian citizenship. According to LRT, a decision on his dual citizen is due over the next couple of weeks.
The residence permit case was heard behinds closed doors.
The ruling can still be appealed with the Supreme Administrative Court of Lithuania.