Hosni, who has been Egypt's culture minister for the past 22-years, has caused concern among some after he was quoted as saying he would burn Hebrew-language books.
He has also been associated with media censorship in his home country and sparked anger among Muslim groups there when he said the hijab was a "step backward" for Egyptian women.
Ursula Lindsey, a freelance journalist who recently interviewed Hosni, said the Egyptian was a controversial candidate, even in his home country.
"He seems regularly to get involved with one controversy or another ... he has many enemies and many critics here [in Egypt], both among Islamists and leftists," she told Al Jazeera.
"A common criticism is that his real loyalty lies with the regime, rather than with intellectuals and artists and that his decisions are politically based rather than to really foster culture."
Hosni has apologised for his comments about burning Hebrew books, saying the comments were taken out of context, and his ministry has been restoring synagogues in Cairo - a move some people see as an attempt to win favour with the Unesco.
Kenneth Luis, the permanent delegate of Malaysia to the UN body, told Al Jazeera that the issue of Hosni's alleged anti-semitism "has been sorted out".
"We believe that a person coming from the Arab world should be given the opportunity to run this organisation," he said.
As the voting progressed, other candidates in the running for the top job at Unesco dropped out.
Benita Ferrero-Waldner, the EU external relations commissioner, pulled out of the race on Sunday and Ivonne Baki, the Ecuadorian candidate, withdrew late on Monday.
Unesco, the United Nations educational, scientific and cultural organisation, provides protection of world heritage sites, as well as working in the areas of education, press freedom and "respect for shared values".