Brazilian media have said that the players are owed three months' wages and five to six months' image rights.
Botafogo's debts at the end of 2013 totalled 700 million Reais (182 million pounds) and its accounts have been frozen by authorities. The club has already warned that it could be forced to pull out of the Brazilian championship.
"Botafogo has gone into collapse and cannot get out of the situation," Mancini, who said he has not been paid for four months, told Radio ESPN.
"Today, I came across a situation which I have never seen in 30 years of football, where part of the squad got paid and another part did not.
"When I arrive for training, I find a heavy atmosphere instead of happiness and motivation," he added.
"It gets more and more difficult every day. You don't want to come to a football club in a country which has just hosted the World Cup and have to live with this.
"The players have told me they won't leave the club... but you never know what each one's limit is. Everyone is fed up and it's a negative environment."
Brazil's clubs are plagued by financial mismanagement and last month the Ministry of Sport said they owed a total of 4 billion Reais in unpaid wages, taxes and social security contributions.
Botafogo dropped into the Brazilian championship relegation zone after losing 2-0 to Atletico Paranaense at the weekend.
(Reporting By Brian Homewood; editing by Sudipto Ganguly)
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