David Simpson, the state-owned concern's route managing director for Scotland, has been absent since shortly after a meeting with a representative of his London bosses earlier this month.
Officials at Network Rail have refused to discuss the reasons for his departure.
When asked, an official spokesman said: "David Simpson is currently on a period of extended leave owing to personal circumstances."
Mr Simpson has run Network Rail north of the border since 2005, which has had considerable devolution in its business since October 2011 - reflecting political devolution at Holyrood, which is responsible for transport.
The Blantyre-born executive, who is understood to live in Ayrshire, is a veteran of the old British Rail and has spent more than 25 years in the industry. He served in senior roles in England for Railtrack, the semi-privatised rail infrastructure firm that predated Network Rail, and in rail freight firms.
He managed the UK's most important single railway, the West Coast Main Line from Glasgow to London via Manchester and Birmingham before securing the top Scottish job in 2005.
At the time of publication, Mr Simpson could not be contacted for comment.