Alexander Van der Bellen, who made the statements while speaking to students on Monday, began by stating that he believes it is "every woman's right to wear whatever she likes."
However, referring to discrimination against Muslims in Austria, the leader went on to state that "if this continues... with the widely spreading Islamophobia, the day will come when we have to ask all women to wear a headscarf – all – out of solidarity to those who do it for religious reasons."
Van der Bellen's statements, which were broadcast by ORF, did not sit well with some people on social media.
One person took to Twitter to express his disappointment with the large number of women who voted for Van der Bellen, considering his latest statement.
The backlash prompted the president to defend his words in a Wednesday Facebook post, in which he stressed that women who wear headscarves are often subjected to "public hostility" in Austria.
Meanwhile, other politicians across Austria have been outspoken about their views on headscarves – which don't at all align with Van der Bellen's opinions.
Last month, several government officials sharply criticized a recommendation by the Islamic Religious Community in Austria (IGGO) that Muslim women start wearing a headscarf from the onset of puberty, with the country's secretary of state, Muna Duzdar, saying she "deeply" rejects headscarves.
Van der Bellen's comments come less than three months after the Austrian government announced plans to ban full-face veils in public, a move which prompted a demonstration in the capital, Vienna.
Islamic garb has long been a topic of debate in Europe, with the European Court of Justice (ECJ) ruling last month that employers can ban such attire under general rules which prohibit visible religious symbols in the workplace.