The amendments constitute a change of the state system, for which there is "no justifiable and acceptable reason or necessity", a statement from the president said.
At present, parliament elects the president for a non-renewable seven-year period.
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"Whatever system the Turkish majority want should be done through elections"
Baz, Vancouver, Canada
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Plans for Turkey's president to be directly elected by the people for a five-year term, and renewable for a further five years, were backed earlier in May by more than two-thirds of members in the 550-seat assembly.
The ruling AK Party tried to push through the reform in a direct appeal to voters after Abdullah Gul, Turkey's foreign minister and the party's presidential candidate, failed to secure parliament's backing to become president.
Recept Tayyip Erdogan, the Turkish prime minister, had already said that his government would push the planned reform through parliament, unchanged, for a second time if Sezer vetoed the law, possibly opening the way for a referendum on the subject.
Sezer cannot veto legislation a second time if it is unchanged; he must either approve the law or call a referendum.