The official however, would not say how many of the freed inmates Turkey would take, or when they would arrive, saying those details would "become clearer in time." The official spoke on condition of anonymity in line with government rules that bar civil servants from speaking to journalists without prior authorization.
Private NTV television said 10 Palestinians were expected in Istanbul. The ministry would not confirm the report but the official said it would be a small number.
Under the prisoner swap deal, 1,027 Palestinian prisoners will be released in return for a captured Israeli soldier, Gilad Schalit.
When Tuesday's exchange is complete, 477 Palestinians held in Israeli jails, including 27 women, will have been released, several of them after decades behind bars. More than 200 prisoners, originally from the West Bank, will instead be sent to the fenced-off Gaza Strip. The final 550 Palestinians are due to be freed in about two months.
Turkey last week welcomed the prisoner swap agreement and declared it was ready to contribute to the deal.