He said the army will not "be deterred by such attacks" and will continue to defend the basic tenets of the republic set out by the country's founding father Mustafa Kemal Ataturk in 1923.
Anniversary speech
Buyukanit's message was issued to mark the 85th anniversary on August 30 of a decisive victory for Turkish forces led by Ataturk in its independence war against invading foreign powers in 1922 and which was crucial for the establishment of modern Turkey.
Despite the military's misgivings, Gul is likely to become Turkey's 11th president after a third round of presidential voting in the parliament on Tuesday.
Recep Tayyip Erdogan, the Turkish prime minister, had picked Gul as his candidate and subsequently called early general elections to defuse tensions.
The elections were held on July 22, and Erdogan's AK party won a resounding victory, which most analysts in Ankara interpreted as the people's support for Gul's candidacy.
Voting process
Gul's attempt to become the president in a parliamentary voting process earlier this year was blocked by the secular establishment because of concerns about his past.
"Nefarious plans to ruin Turkey's secular and democratic nature emerge in different forms everyday"

Yasar Buyukanit,
Turkish armed forces chief
He withdrew in the face of mounting criticism from the secular opposition, which was backed by the military and the top court.
Huge crowds took to the streets in major cities and demanded that Gul revoke his candidacy for the post.
Gul renewed his presidential bid after the elections.
In the first two rounds of voting this month, he failed to get support from two-thirds of the parliament, which was required to be elected for the post.
But he will need only a simple majority in the third round.
The AK party holds 341 of the 550 seats in parliament.
'Nefarious plans'
In his Victory Day statement on Monday, Buyukanit said: "Nefarious plans to ruin Turkey's secular and democratic nature emerge in different forms everyday.
"The military will, just as it has so far, keep its determination to guard social, democratic and secular Turkey.
"The Turkish Armed Forces will not make any concessions ... in its duty of guarding the Turkish Republic, a secular and social state based on the rule of law."
The statement recalled a military warning issued in April during the height of the debate about Gul's bid for presidency.
In the earlier statement, the military said it was concerned about the future of Turkey's secular traditions and hinted it could intervene to guard them.