General Tuncer Kilinc also said he supported Ankara's bid to become an EU member "in line with national interests", but underlined that Turkey should not turn its face only towards the West, but also to the East.
The reforms, adopted earlier this month, limit executive powers and areas of responsibility ascribed to the National Security Council (MGK) - the body through which the generals seek to influence national policy.
"With the reforms, the council ... has kept its place legally, but was left functionless," General Kilinc, the MGK's outgoing secretary general, said in a speech at a handover ceremony.
Secularists vs Islamists
His remarks were the first public criticism of the changes from the military, the staunch guardians of the Muslim country's strictly secular system.
Kilinc said he had personally raised objections to the reforms while they were being drawn up because they would harm "national interests".
The general specifically mentioned one reform which paved the way for the appointment of civilian officials as future MGK secretary generals, a post which has only been held by senior generals so far.
"I am handing over my post which I am greatly concerned could be politicised ... under the administration of a civilian secretary general," Kilinc said.
Kilinc is being replaced by another general, Sukru Sariisik, who was appointed to the post two days before the president approved the EU-minded reforms.
Turkey should keep its options open for other regional partnerships, especially with Russia and Iran.
General Tuncer Kilinc,
Former secretary-general, MGK
These also limit the duties of the MGK secretary general to secretarial organisation, reduce the council's meetings from one month to every two months and emphasise that its decisions are not binding for the government.
Limiting the army's powers is a task of particular difficulty for the governing Justice and Development Party, whose leaders - including Prime Minister Recep Tayyip Erdogan - are under scrutiny by the secular elite for their Islamist roots.
But the reforms have been hailed by the European Union as a major step in Ankara's efforts to catch up with European norms.
Turkey, the laggard among 13 EU-hopefuls, has yet to secure a date from the European Union for the start of accession talks although Brussels is due to review its progress at the end of next year.
Kilinc said Turkey's possible membership of the European Union would benefit the country's security, but noted that Ankara should watch its national interests as it strives to join the EU.
But, he also said, Turkey should not ignore the possibility of not winning EU membership and should keep its options open for other regional partnerships, especially with Russia and its eastern neighbour Iran.
Good ties with these two states would enable Turkey to have more influence in the energy-rich Caucasus, Kilinc said.
"I believe we need these good ties even if we become a full member of the European Union," he added.
Kilinc had caused a controversy in 2000 when he first spoke in favour of closer ties with Iran and Russia, but he also said such cooperation could not be an alternative to Ankara's west-oriented path.