In a letter dated 15 January to the Speaker of the House Mark Shelton and President of the Legislative Council Craig Farell, Tasmanian Greens Leader Rosalie Woodruff branded the decision as "deeply disrespectful of the Tasmanian Aboriginal Community."

"We understand the desire to mark the proclamation of Mary Donaldson as Queen of Denmark," she said.

"This should not, however, take precedence over our duty to pay our ongoing formal respect to Tasmanian Aboriginal people and their pre-existing, and enduring relationship with this island."

The Aboriginal flag has now been reinstated.

The Premier Jeremy Rockliff and speaker responded to the criticisms on Tuesday morning.

Mr Shelton said that he and Mr Farrell had agreed to fly the Danish flag for one day at the request of state protocol "in recognition of the connection now between the Danish people and Tasmania."

When asked why the Aboriginal flag was removed, Mr Shelton said there are only three flag poles and the flags were flown according to "national protocol"

National Flag protocol states the order of precedence for flags after the Australian National Flag is the national flag of other nations, state and territory flags, other Australian flags prescribed by the Flags Act 1953, ensigns and pennants.

Mr Shelton was asked if they'd considered if the decision was hurtful to the Aboriginal community.

Mr Shelton said: "The request was for one day to recognise a special day that was happening with the connection between the Danish and the Tasmanian people."

"Understand the Aboriginal concerns, but it was one day and the Aboriginal flag is back up and flying there," he said.

The Premier concurred saying "in line with national protocols, the Danish flag was installed for one day".

"The Aboriginal flag has been reinstalled now as appropriate."

However, Dr Woodruff said the speaker and president "can't hide behind protocols to justify their disgraceful decision".

"They made an active choice to remove the Aboriginal flag from the Tasmanian Parliament, and replace it with the Danish flag."

If 'flag' protocols meant removing the Aboriginal flag, "then their obvious decision should have been not to go ahead with flying the Danish flag".

Dr Woodruff said there was "no excuse" to remove the flag as Parliament was already being lit up in the Danish colours of red and white.

The Tasmanian Aboriginal Centre has been contacted for comment.