Spanish construction and engineering firm OHL, one of the companies behind the project, refuses to remove sand for free in a letter sent to its consortium partners which was published Tuesday by news site El Confidencial.
In 2011, Saudi Arabia awarded the contract worth 6.7 billion euros ($7.4 billion) to the consortium of 12 Spanish companies and two Saudi firms for a project which aims to improve transport connections during the annual hajj pilgrimage.
The contract is for laying the 444 kilometres (275 miles) of track between the two cities as well as supplying 35 trains and operating and maintaining the line for 12 years.
The leading firms in the consortium –- train maker Talgo, state-run train operator Renfe and state track operator Adif – have extensive experience with Spain's own high-speed network, the world's second largest after China's.
The Saudi project is the first such line to be built across a desert. The rail line crosses the Arabian Desert, where sandstorms are frequent and large dunes can suddenly form.
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In a copy of the letter dated February 7 which was seen by AFP, OHL said it was not "paid to clear the track of sand in order to facilitate the work of other consortium members."
Talgo wants to start test runs of its trains on the track.
OHL said it was "very willing to carry out extra works to clear the tracks" but only after an agreement with the other members of the consortium is signed spelling out what its exact responsibilities would be.
OHL declined to comment on the publication of the letter.
Public Works Minister Ana Pastor, who visited the work-in-progress in 2014, downplayed the row.
"We knew from the beginning what we would find. This is not a new question and it is up to Spanish engineers to solve this challenge," she told reporters.
The high-speed railway was initially scheduled to open at the end of 2016 but the deadline for its completion has been moved to the end of 2017.