The newspaper had reported that while the special inquiry into the killings recommended the prosecution of 10 people only five faced trial and were later executed. No action was taken against Mr Tsikata.
Mr Tsikata, right-hand man to Flt Lt Jerry Rawlings, Ghana's military ruler, says he was defamed because the story failed to mention that a public tribunal and the country's attorney-general later ruled there was not enough evidence against him to prosecute.
At the High Court in London Richard Dowden, the Independent's diplomatic editor, denied the statement concerning the judges' execution in 1982, contained in a report on the 1992 elections to return Ghana to democratic rule, had been 'biased'.
He said that in covering a regime where people were being executed it was no surprise that the findings of an independent inquiry, led by a former chief justice, were given more weight than comments made later by the country's attorney-general.
'It would have been an exceedingly brave man who would have recommended proceedings against his own government,' he said.
Mr Dowden said that when he visited the country in 1987 there was still a 'state of terror . . . linked to the name of Kojo Tsikata. People did not bandy his name around. They were very, very frightened of him'.
Dr Stephen Ellis, former West Africa researcher for Amnesty International, said the human rights organisation produced a report critical of the country's public tribunal system. Sydney Kentridge QC, for the Independent, said rulings by the public tribunal could not 'supersede' the earlier inquiry reports. He read testimony from a member of the Ghanaian Bar who said that the tribunals were mere 'kangaroo courts'.
Mr Kentridge also questioned the relevance of a tape recording in which one of the five prosecuted for the judges' murders withdrew allegations that Mr Tsikata was involved. He pointed out that the tape was made by a close associate of Flt Lt Rawlings just before the man faced a firing squad.
The Independent contends its report of the inquiry's findings was 'fair and accurate' and covered by privilege. Michael Tugendhat QC will present deputy judge Jonathan Sumption QC with the evidence for Mr Tsikata today. The case is expected to end tomorrow.