Questions about a troubled Malaysian state investment fund and missing money in the Middle East have widened to include nearly $1 billion more.

The Wall Street Journal reported last week that officials in Abu Dhabi were trying to understand why a $1.4 billion transfer that the fund, 1Malaysia Development Bhd., said it made to a counterparty in the Middle Eastern emirate wasn’t received. Now, those officials are questioning a further $993 million that 1MDB reported it paid to the Abu Dhabi fund, the International Petroleum...