Defiant Roy Bennet was going to attend the swering in ceremony but Eddie Cross chose to withdraw from his appointment after a bunch of hooligans believed to be CIO operatives visited his home on Wednesday night.
The arrest did not stop the ceremony from going ahead.
But it could increase tensions between President Robert Mugabe’s ZANU-PF and new Prime Minister Morgan Tsvangirai’s MDC soon after they ended months of deadlock in negotiations and agreed to implement a power-sharing deal.
"Roy Bennett was arrested a few minutes ago at Charles Prince Airport. I am not sure whether he was arriving or leaving," Ian Makone, a senior MDC official told Reuters.
Police were not immediately available for comment.
Bennett, the MDC Treasurer General, was nominated as deputy minister of agriculture by Tsvangirai.
Bennett has been living in exile in South Africa after fleeing the country about two years ago because police wanted to question him in connection with the discovery of an arms cache in eastern Zimbabwe.
The MDC said Bennett was taken to what it called a "notorious torture and interrogation base".
Troubles initially emerged at the swearing-in proceedings.
MDC ministers refused to rehearse the oath-taking ceremony, saying Mugabe had appointed two more ministers than his party had been allocated under a power-sharing agreement aimed at rescuing Zimbabwe from economic collapse.
But Mugabe later began swearing in cabinet ministers.
Mugabe and Tsvangirai agreed last September to share power, but the deal stalled for months as they haggled over the allocation of cabinet posts, stirring doubts over whether the old foes can work together to bring in foreign aid and investment.