Last month, football’s world governing body made the move in a bid to improve governance within the Confederation of African Football (Caf).
“This can be considered as a new aspect of colonialism,” the Swiss told BBC Sport in a statement.
“Fifa’s direct intervention to Caf and sending Mrs Samoura as a kind of ‘supervisor’ ignores the statutes of the federation.
“To recall, confederations are not members of Fifa. Only the national associations are.”
Caf’s Executive Committee (ExCo) is set to discuss Samoura’s looming arrival when it meets in the Egyptian capital Cairo on Wednesday.
Despite previous claims by both Fifa and Caf that her appointment was ‘unanimously’ agreed by the latter’s Executive Committee, there is still believed to be opposition by certain members of the 22-man board.
BBC Sport understands this opposition could be dropped if Samoura, who is set to start her six-month role – renewable if both Caf and Fifa agree to it – from 1 August, would answer to the ExCo rather than Fifa president Gianni Infantino and Caf president Ahmad, as previously mooted in a memo.
Should the latter scenario play out, Samoura and her team of advisors would sit above the ExCo in terms of any decision-making.
“It seems that only Tanzania’s Leodegar Tenga realises the consequences of this action,” added Blatter, who ran Fifa between 1998 and 2015.
“He warns the Caf Executive Committee not to agree to the appointment of Mrs Samoura.”
Blatter was referencing Caf ExCo member Tenga since comments the latter made on a private WhatsApp group with Caf President Ahmad and fellow ExCo members were leaked to the media last month.
While there was an agreement ‘in principle … to the cooperation between Fifa and Caf’, Tenga wrote, ‘we also agreed that Exco members would be given time to go through the proposed text and come up with the details.’
During the ongoing Africa Cup of Nations in Egypt, Caf secretary general Mouad Hajji outlined the advantages he believes Samoura will bring to the organisation.
“This is a great opportunity for Caf to benefit from her expertise,” he told reporters.
“Madame Fatma will arrive with a group of experts, so this will only speed up the process of reform being led by President Ahmad and the ExCo with principles such as good governance, transparency and fairness.
“So we see all this in a very positive way.”
Samoura and Ahmad know each other well from the former’s time in Madagascar, where he headed up the local FA and she served as the United Nations Resident Coordinator from 2010-2016.
Fifa has stated that it will undertake a full forensic audit of Caf, whose president Ahmad has been under scrutiny this year.
While both Fifa and French authorities are investigating him, the BBC revealed on Monday how he claimed expenses from Caf while claiming to be in two different countries at the same time.
The 59-year-old, who has previously denied any wrongdoing, has said he would give his answers for Fifa.
Guinea-Bissau FA president Manuel Nascimento, who does not sit on Caf’s ExCo, believes there is considerable opposition to the Samoura proposal, which is unprecedented in Fifa’s 115-year history.
“I can tell you that the majority of FA presidents oppose Fatma (coming in),” Manuel Nascimento told BBC Sport Africa on Monday.
“None of them, none of us – even me – we don’t want Fatma to come. Because this is Caf. This belongs to Africa.”
“We need reform to be done. However, whatever happens, the reforms should be done in Caf.
“What is supposed to be happening from 1 August will not be accepted in any confederation in the world, so why should we accept it?”
The president of European football body Aleksander Ceferin has also previously expressed his opposition to the plans, questioning the lack of official support from the Caf ExCo, possible conflicts of interest and whether the proposal complied with both Fifa and Caf statutes.