The NIO said it obtained permission from Queen's University to use the image of Mr Heaney, who died in 2013 aged 74.
Glenn Patterson, director of the Seamus Heaney Centre, insisted that consent to use the image did not come from him.
In a letter to The Irish Times newspaper, Professor Patterson wrote: "The Seamus Heaney Centre does not own the portrait of Seamus Heaney that the Northern Ireland Office has used in its Telling Our Stories: NI Beyond 100 campaign.
"The centre could not have given permission for its use and even if it could have, would not have done so, nor would it do anything that involved Seamus Heaney's name, without first consulting the Heaney family."
The NIO insisted that permission from Queen's University was granted.
A spokesperson said: "Our Story in the Making: NI Beyond 100 was created to recognise the stories of the people of Northern Ireland from all communities, past and present.
"Permission for use of the Seamus Heaney portrait was granted by Queen's University Belfast, which holds rights to the portrait."
SDLP leader Colum Eastwood last week slammed the "cynical" use of Mr Heaney's image in Northern Ireland's centenary campaign as "deeply offensive".The Foyle MP told this newspaper: "Heaney's significant body of work belongs to everyone on this island.
"It is his account of life in a place struggling with its own identity and it would be wrong, therefore, to attempt to associate his image with a particular political narrative."
Unionists criticised Mr Eastwood over his comments, including First Minister Arlene Foster and UUP leader Steve Aiken.
Mr Heaney, who was from a Catholic nationalist background, famously wrote the poem An Open Letter in 1983 as a response to being included in The Penguin Book of Contemporary British Poetry.
However, he was pictured with the Queen at a state dinner in Dublin in 2011.