After placing third in the 2012 Reporters Without Borders Press Freedom Index, the country fell to 11th place this year.
Estonia has been ranked by the Paris based NGO since 2003, reaching number three in both 2007 and 2011, while the low came in 2003, when Estonia occupied the 12th position.
The publisher offered no explanation to Estonia's fall.
But director of the Estonian Newspaper Association Mart Raudsaar told Postimees that there are three likely main reasons for the fall. Legislation against hate crimes has been made more strict and it might now be used to quell the media, he said.
“A second reason was that, last year, a number of politicians spoke up on the use of language by journalists, especially those employed by Estonian Public Broadcasting. The talk was that it should somehow be regulated,” added Raudsaar.
The third reason was the high number of attacks on and criticism of the self-regulatory institutions of the media.
Finland, the Netherlands and Norway topped the chart this year and, along with Estonia, also last year.
Other Baltic nations traditionally fare much worse with Lithuania coming in at 33rd, dropping three places while Latvia leapt 11 spots ahead to 39th.
The lowest three nations in the 179-country ranking remained the same with Eritrea dead last, and North Korea and Turkmenistan the other bottom dwellers.
The index considers six criteria: the degree of opinions represented in the press, media independence from authorities, the environment in which journalists work in, legislative framework, transparency and infrastructure.