In its ruling that is final and not subject to appeal, the Lithuanian Supreme Administrative Court also ordered the Road Administration to pay Zabulionis almost 30 euros in compensation.
According to the court, the administration failed to prove during its investigation that the man committed official misconduct.
Transport Minister Rokas Masiulis says that officials with dubious reputation cannot work at the administration.
"The court's ruling has created an ambiguous situation. The person is suspected of having coordinated the terms and conditions of tenders with the contractors and receiving a payment from them for that," the minister said in a comment.
"I do not think that people whose reputations was thus stained can work in road building," he added.
Law-enforcement officials suspect that Zabulionis obtained the high-ranking post at the Road Administration with the help of Raimondas Kurlianskis, vice-president at MG Baltic, one of Lithuania's largest business groups.