Hundreds of Turkish students ignored police warnings and marched across Istanbul on Wednesday to protest President Recep Tayyip Erdogan's appointment of a loyalist as the head of a top university.

The second demonstration in three days against Erdogan's pick for Bogazici University delivered a rare challenge to the Turkish leader since he cracked down on dissent after surviving a coup bid in 2016.

More than 1,000 people scuffled with police on Monday to protest Erdogan's appointment of Melih Bulu -- a losing candidate from the ruling AKP party in the 2015 general election -- as rector of the prestigious public institution.

Turkish anti riot police officers stand guard at the main gate of the Bogazici university on in Istanbul during a protest against the appointment of the new rector by the Turkish president.
Turkish anti riot police officers stand guard at the main gate of the Bogazici university on in Istanbul during a protest against the appointment of the new rector by the Turkish president. AFP / Ozan KOSE

Turkish police responded by arresting 36 people in a series of raids that began in the early hours of Tuesday.

They then fenced off the university and handcuffed its gates to avert a planned rally by students and their supporters on Wednesday.

Organisers regrouped and decided to hold a protest march instead that they coordinated through social media.

Hundreds walked chanting and holding up slogans along the Bosphorus before boarding a ferry and crossing to the Asian side of Istanbul for a rally attended by a crowd that AFP reporters estimated at more than 1,000.

Students show their IDs to enter the campus as Turkish anti-riot police officers guard the main gate of the Bogazici university on January in Istanbul during a protest against the appointment of the new rector by the Turkish president.
Students show their IDs to enter the campus as Turkish anti-riot police officers guard the main gate of the Bogazici university on January in Istanbul during a protest against the appointment of the new rector by the Turkish president. AFP / Ozan KOSE

Anti-riot police watched without intervening along the route.

"To walk together on such a day of defiance makes us feel very good," said student Zehra Aydemir.

"I am proud that my friends and I were able to meet up and fight for what we want," added university graduate Cinar Cifter.

Hundreds of students protest the Turkish president's appointment of new rector to Bogazici university in Istanbul. Turkish police detained 36 people.
Hundreds of students protest the Turkish president's appointment of new rector to Bogazici university in Istanbul. Turkish police detained 36 people. AFP / Ozan KOSE

The march attracted a mixed but overwhelmingly young crowd that held up political posters and waved rainbow flags in support of LGBTQ rights.

Some danced around to the sounds of Metallica -- an ironic refence to a TV interview Bulu gave Tuesday in which he claimed to listen to the US heavy metal group.

One placard referred to Erdogan as "Master of Puppets" -- the name of a 1986 Metallica album and song -- while another cited the band's iconic refrain: "nothing else matters".

Erdogan has not referred to the protests in public.

But Turkish officials are keen to avoid a repeat of 2013 Gezi Park protests that began as a defence of a small green space in the heart of Istanbul before morphing into the first serious challenges to Erdogan's rule.

Erdogan's ruling coalition partner Devlet Bahceli of the ultranationalist MHP party said the protests "need to be crushed" before they grow any further.

"Those who are trying to strangle Turkey by taking this rector's nomination as an excuse are terrorists' pawns and separatists dressed as students," Bahceli said Wednesday.

The protesters were "trying to create a new Gezi uprising," Bahceli said.

Rectors for Turkey's universities were appointed through elections from the 1990s to July 2016.

Bogazici University has traditionally been a stronghold of leftist causes that made into a government's target on past occasions.

Several of its students were arrested after a demonstration against Turkey's military offensive in Syria in 2018.