Indonesia has in recent years seen its long-standing reputation for religious tolerance come under scrutiny as "hardline Islamic groups" muscle their way into public and political life in the young democracy.
The vast majority of Indonesians practice a moderate form of Islam and the country has sizeable minorities of Hindus, Christians, and people who adhere to traditional beliefs. Religious diversity is enshrined in its constitution.
The survey by a Jakarta-based organization polled over 4,200 Muslim students, mostly in top schools and universities on Java island, home to over half the country's population.
Nearly one in four students said they were, to varying degrees, ready to wage "jihad" to achieve a caliphate.
"This indicates that intolerant teachings have already entered top universities and high schools," pollster Alvara, which carried out the survey, said in its report released Tuesday.
"The government and moderate Islamic organizations must start taking tangible steps to anticipate this and be present in student circles with language that is easy for them to understand," the report added.
A presidential spokesman declined to comment on the findings.
"Hardline Islamic groups" late last year led mass street rallies against Jakarta's former governor, a Christian, whom they believed had insulted Islam. They eventually succeeded in derailing Basuki Tjahaja Purnama's re-election bid in April this year, and he was subsequently jailed for blasphemy. The ruling was criticised globally as unjust.
Groups like the Islamic Defenders Front (FPI) call for sharia law to be imposed on the country and believe its leaders should only be Muslim.
The survey showed that the vast majority of students disagree with the establishment of an "Islamic caliphate" and violence.
But authorities have repeatedly warned against the creeping influence of extremist thought among student organisations and in campus activities.
President Joko Widodo and his government are trying to contain the rising influence of hairline groups, especially in universities and Islamic boarding schools.
A presidential decree banning any civil organisations deemed to go against the country's secular state ideology was approved by parliament last month. Hizb-ut-Tahrir, a largely peaceful organisation that calls for the establishment of a caliphate in Indonesia, was the first group to be disbanded under the decree.
President Widodo has made several speeches at Islamic boarding schools around the country emphasizing Indonesia's diversity and the importance of national unity.
In September, Widodo called at a conference of around 3,000 university rectors for the promotion of the country's secular ideology, 'Pancasila', in education.