Nguyen Ngoc Dong and Nguyen Nhat received reprimands from Prime Minister Nguyen Xuan Phuc on Wednesday while Nguyen Van Cong got an official warning.
Nguyen Hong Truong has been retrospectively stripped of his position as Deputy Minister of Transport for the 2011-15 and 2016-17 terms.
The Communist Party had meted out similar punishments to them in July.
According to the Communist Party's secretariat, Truong was responsible for violations committed by the ministry's Party Affairs Committee during his time as a member of the committee, deputy minister and head of the ministry's Steering Committee for Enterprise Innovation and Development.
He was also found to be personally responsible for approving enterprise values and equitization plans for many companies and units under the transport ministry and seeking the government's approval for equitization plans, none of which was within his powers and were also in contravention of the law.
The Party's Central Inspection Committee found Dong, Nhat and Cong in flagrant violation of the principle of democratic centralism and working regulations. They were also found to have been irresponsible and lax in their leadership and oversight, which allowed many violations related to equitization to occur at a number of companies under their ministry.
A sweeping corruption crackdown by party chief and President Nguyen Phu Trong has snared scores of high-profile officials in the last three years.