"We are worried that a press agency, which used to be trusted by professionals and by the public, is becoming instrumentalised by politicians," IFJ President Jim Boumelha said in a news release.
EFJ President Arne König urged the management of the Ukrainian agency, UNIAN, "to respect professional standards and stop the ongoing harassment campaign against the staff."
Concerns about interference began last year, when new managers took over the agency and ousted the editor, Alexandre Kharchenko.
Since then, journalists have complained of undo pressure from management and delayed salaries. Several journalists quit the agency earlier this month.
Meanwhile, the opposition party headed by imprisoned former Prime Minister Yulia Tymoshenko has accused the agency of false reporting.
Journalists have also complained to EurActiv that the agency has collaborated with the authorities in news coverage.
"Not only is the UNIAN News Agency losing money, but its conversion into one more voice for Ukrainian authorities will do further damage to media freedom in Ukraine" Yuryi Lukanov, president of the Independent Media Trade Union of Ukraine, said in a statement issued by the IFJ.
Ukraine has been under fire by press freedom groups in recent months. In September, the Parliament voted to criminalise defamation, although the bill was later withdrawn amid protest from free-speech and human rights groups.
Government tax authorities launched an investigation of TVi, the New York-based Committee to Protect Journalists reported. The investigation was later dropped but rights advocates accused the government of trying to intimidate the opposition broadcaster.
UNIAN News Agency is one of four biggest news agencies in Ukraine and has gained a reputation for its solid political reporting.
Its main competitors are the state-run Ukrinform, the privately owned Interfax-Ukraine and the Ukrainian News Agency, which is part of the Inter media group.