Standing up to object, Prakash said he along with journalists Swapan Dasgupta and Kanchan Gupta who were among the audience "take very strong exception to the presentation of India".
Jose had claimed that "a hundred Christ were murdered in India" and that "the RSS engineered the pogrom against the Sikhs in 1984".
An agitated Prakash said that if the audience at the conference "were to leave with this picture of India, then democracy would be in grave danger".
"We are the largest and most vibrant democracy in the world. We have 900 million electors, 600 million of whom have just voted. We are the most diverse society in the world, not just social and economic, but political," he added.
He said Jose's presentation had "very major factual inaccuracies, which need to be corrected".
Prakash said he had himself covered the 1984 riots as a journalist and that the media in India is "most free and vibrant".
He said the Indian media has covered "every social atrocity and social friction in the country" and reiterated his protest against "this kind of branding of India".
"There are some people in the world who are uncomfortable with the electoral decision taken by the 600 million voters of India, and are using forums like this to push their own political agenda. I seriously protest," Prakash said.
The Prasar Bharati chief said the Indian media is "very sensitive to issues relating to the minorities" and the claim that the media is one-sided is false.
The conference was organised jointly by the governments of the UK and Canada.
"I am pained by the decision of the organisers to have given a platform for such a blatantly anti-India presentation. I don't think anyone is furthering the cause of democracy by running down the most vibrant democracy in the world," he said.
Prakash said some time ago there were race riots in some parts of the US, but that cannot be taken as an example to brand America as a non-democratic nation or a racist nation.
Speaking on the sidelines of the conference, he said: "Those who raise a question mark about press freedom in India must be stone deaf. If you see the cacophony during the recent parliamentary elections, the hurl of abuses that political leaders and the abusive attacks that went on - both at the national level and the states - and it was unabated, and remains unabated in the social media even today, and gets echoed in the mainstream media. What are they talking about?"
"In fact the present political leaders of the country from across the parties, there are a large number of them who have fought for restoration of press freedom and democracy in the mid-70s in this country, and for them democracy is very dear. When we talk of plurality of news media in India, it is unprecedented."
( With inputs from IANS )