In comments to constituents in Hanoi, Mr Trong outlined the rationale behind the recent purge of a prominent intellectual, Chu Hao, who was accused of violating party dogma.
He said that independent political thinking was very dangerous and that some people needed to be disciplined as a warning to others.
Chu Hao, a publisher and former deputy science minister, resigned from the party after 45 years as a member after being accused of serious wrongdoing.
He appears to have angered the leadership by publishing translations of works that criticised authoritarianism and the abuses of one party states.
Mr Trong denounced what he called “self evolution”, party jargon for independent thinking.
He said that there was no way of knowing where members who embarked on such a journey would end up, and stressed the need to stabilise politics.
The comments are in line with his reputation as a hard line ideologue who believes rigid discipline is needed to stifle debate about political reform.
In recent years, the Vietnamese Communist party had tolerated a degree of internal political debate about the merits of a more open political system.
Some of the books that got Chu Hao into trouble were published in Vietnamese translation more than a decade ago.
The decision to move against him came just days after Mr Trong assumed the post of state president in addition to his existing role as general-secretary of the Communist party.
Nguyen Phu Trong has attempted to reinforce the central role of the Communist party and crack down on dissent inside and outside the party since he secured a second term as party leader in 2016.
His drive for ideological purity has been matched by an anti-corruption campaign which has targeted alleged offenders from all levels of the party and state run enterprises.