Jeff Highfield, formerly employed by Bishopsgate Investment Management, told the Old Bailey fraud trial that he was told by former Maxwell aide, Larry Trachtenberg, there was "confusion" over the ownership of the shares. Mr Trachtenberg allegedly said the situation needed to be resolved.
Mr Highfield believed the pension-owned stock had been used as part of a share lending programme to raise funds for the Maxwell empire.
He said he was eventually told that 22 million shares in Israeli company Teva had been charged to a bank after Mr Maxwell's death on 5 November 1991.
The prosecution alleges the shares were pledged in a fraudulent bid to prop up the struggling Maxwell dynasty.
Mr Highfield said he discovered in the month Robert Maxwell died that there were stock transactions that did not appear to be accounted for.
He asked Mr Trachtenberg about his discovery and was assured the confusion over Teva shares would be resolved. He added that the Maxwell director, a defendant in the long-running trial, gave no clue to the location of the missing stock.
Before the empire crashed, Mr Highfield made unsuccessful attempts to prevent ownership of the stock being re-registered and tried to secure BIM's rights over the shares. He was advised by Teva that the shares had been pledged with the signed approval of BIM.
In the dock are Kevin Maxwell, his brother, Ian and Mr Trachtenberg, who all deny conspiracy to defraud the pension funds by misuse of its investments.
The trial was adjourned to today.