The award winning editor-in-chief, Geoff Nyarota, left on Monday saying he had resigned.
But Tuesday's issue led with a story saying he had been relieved of his duties "with immediate effect".
The Daily News has been a strong critic of President Robert Mugabe's government, and is the best selling newspaper in the country.
Neither the newspaper's owners, Associated Newspapers of Zimbabwe, or Mr Nyarota have explained the reasons for his departure.
Mr Nyarota has been arrested by police several times and has won numerous awards for journalism and press freedom. He helped found the newspaper in 1999.
"It was not an easy decision. It breaks my heart," he said on Monday.
A strike by journalists over pay began before Christmas. The Daily News web site has not been updated since 19 December.
Deadline
His departure comes at a precarious position for independent journalists in Zimbabwe.
They await a decision by the government's media commission on who will be allowed to work in the country.
New draconian press legislation was introduced at the start of the year which holds that journalists publishing falsehoods or undermining the credibility of President Mugabe can be heavily fined or liable to a two-year prison sentence.
Media and Information Commission chairman Tafataona Mahoso told the state-run Herald on Tuesday that it would start issuing new press accreditations in the first week of January.
Already a number of foreign media organisations, including the BBC, have been prevented from entering the country on reporting trips.
The arrest and intimidation of independent journalists has become commonplace.