The report, meant to have been released on Wednesday, was held back as Nqakula and Justice Minister Penuell Maduna were "not satisfied with certain aspects" of it.
Nqakula's spokesman Leslie Xinwa said on Thursday the ministers wanted to "engage the committee of inquiry, who compiled the report, on certain issues".
"They (the ministers) did not specify what the problem was exactly. They just said they want to meet with the committee and discuss the issues," Xinwa said.
The Johannesburg daily, Beeld, reported though that, according to a copy of a section of the report in its possession, the main motive for farm attacks was robbery.
According to advocates quoted in the report, racial hatred also played a significant role.
There had also been farm attacks with a political undertone, but these had been in the minority.
The report was commissioned in March 2001 by former safety and security minister, the late Steve Tshwete, after farmers' union Agri SA asked for an investigation into the motives for the attacks.
Agri SA spokesman Kobus Visser on Thursday questioned the independence of the committee.
"We are disappointed that the minister would see fit to refer the report back to an independent committee. This action casts doubt on the integrity of the report."
According to Visser, the minister was unhappy with certain recommendations made in the report.
"The minister's office would not elaborate on the reasons."
He said Nqakula should at least make public the reasons for the delay.
Meanwhile, opposition parties questioned government's motives.
The Democratic Alliance said the delay showed government's opposition to any document that could be regarded as independent.
DA rural safety spokesman Paul Swart said the committee had reportedly recommended that "farmers -- just like people in the urban areas -- must themselves beef up their security". "This statement is a direct indictment of government's failure to protect the safety and security of all South Africans," Swart said.
He said the report should be released immediately as it was "a matter of life or death" for rural communities.
Swart said the original report, including any amended versions of the report, must be made available to the portfolio committee on safety and security for scrutiny.
New National Party justice spokeswoman Carol Johnson said the party was concerned the delay was nothing more than political meddling.
"If the report has now been referred back to the commission because the respective ministers are 'not satisfied' with it, the report can never be said to be independent, and it's credibility will now be tainted," she said.
The Freedom Front said the delay showed that the report could have found that the motives for farm attacks were not merely criminal.
FF safety and security spokesman Pieter Groenewald questioned why the report was being sent back, when Nqakula attributed the motives for farm murders to ordinary crime.
"This creates the impression that the commission has found that the causes and motives for farm murders were more than criminality."
According to estimates by Agri SA, violent robberies and murders on farms increased 11 percent between 1991 and 2001.
It also estimated that 7,424 attacks occurred between 1991 and June this year, and 1,344 people were killed during the same period - Sapa
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