Maharaj said Mo Shaik - Ngcuka's other main accuser before the Hefer Commission - reported this to him in late 1989 or early 1990.
Maharaj told Judge Joos Hefer that Shaik was at the time in charge of the ANC's intelligence operations within South Africa.
Maharaj himself was co-ordinating the former liberation movement's mass struggle within the country as commander of Operation Vula.
Maharaj had infiltrated South Africa illegally and was dependent on the Durban-based Shaik's security briefings to combat the "permanent hazard" of government informers.
At one stage, Maharaj wanted to contact the National Association of Democratic Lawyers (Nadel) and asked Shaik's opinion on the matter.
Shaik warned it would be unsafe because a high-level source within Nadel was believed to have been informing for the apartheid security forces.
Maharaj testified that he felt uncomfortable about this warning because Shaik could give him no reasonable clues as to the identity of the suspected spy.
Shaik therefore investigated the matter further.
During late 1989 or early 1990 Shaik concluded in a follow-up report to him that Ngcuka was "in all probability" the agent operating within Nadel, Maharaj continued.
He added that he did not act against Ngcuka, but relayed the allegation to current deputy president Jacob Zuma.
Zuma was at the time overall head of ANC intelligence and worked outside the country.
Maharaj said he assumed that Shaik would also have sent the information on to Zuma through his own communication channels to the exiled ANC leadership.
Maharaj's long-awaited testimony before the Hefer Commission of inquiry into the spying allegations against Ngcuka is to continue later yesterday.
All the main role players in the spy saga attended yesterday's commission hearing in the Iustitia building in Bloemfontein.
These included Ngcuka, Justice Minister Penuell Maduna, Maharaj, Shaik and journalist Ranjeni Munusamy.
Meanwhile, Maharaj also accused Ngcuka yesterday of several abuses of power.
An indignant Maharaj told Judge Joos Hefer that Ngcuka had defamed him and his wife at this meeting by disclosing confidential information obtained during a Scorpions investigation.
The investigation related to the elite unit's larger inquiry into alleged bribery in government's controversial arms deal.
Maharaj further accused the head prosecutor of making "derogatory racial statements about Indian South Africans" at the meeting, with personal reference to him (Maharaj).
The African National Congress's counsel, advocate Steven Joseph, submitted a 500-page bundle of documents to the commission to support his client's testimony.
This revealed that Maharaj had been keeping records and even transcriptions of relevant telephone conversations since rumours first surfaced that Ngcuka's Scorpions were investigating him and his wife.
Corruption allegations against Maharaj followed a Scorpions raid related to their arms deal investigation at the premises of businessperson Schabir Shaik.
Shaik's seized records of payments resulted in allegations leaked to the media that Maharaj had received kick-backs during his ministerial tenure for state contracts awarded to Shaik.
Maharaj denied this again yesterday in his testimony before Hefer.
He stated that the relevant payments were made to his wife for her work as a consultant to Shaik's companies. – Sapa.