Workers must reply 'yes' to a text message from the NSW Rail, Tram and Bus Union to support calling off a proposed 24-hour strike on Monday, with a non-reply counted as a 'no' vote.
However, many workers posted on the RTBU Facebook page on Wednesday morning saying they were still to receive the text just hours before the midday deadline.
"I would like to know why this has been sent out as an SMS. There are many of us on leave at the moment that do not have our work phones with us. Also how are we going to be able to vote if we are on leave," one said.
"I didn't get one either. What number do we call to make sure our phone numbers are right," another asked.
With more than 9000 workers due to stop work on Monday, the RBTU confirmed to AAP about 6500 members had received the text.
Transport Minister Andrew Constance said the vote on Sydney Trains' latest offer to workers seemed designed to fail.
"There is so much riding on this strike action, I would find it unbelievable that they have potentially used a process around this that is designed to fail," he told 2GB.
"Due to the large number of texts sent last night we understand that some have not reached members," the RTBU said on its Facebook page.
While the ballot will determine whether or not Monday's strike proceeds, it is too late to stave off major disruptions on Sydney's rail network on Thursday, according to Mr Constance.
Services will be cut from 2900 during weekdays to 1600, due to industrial action placing an indefinite ban on overtime.
Premier Gladys Berejiklian is urging commuters to check timetables and to avoid travelling during peak hour.
Mr Constance says trains will operate on a Saturday schedule, cutting services across the state on Thursday and Australia Day on Friday.
"Tomorrow is going to be disruptive," he said on Wednesday.
The union initially wanted a six per cent pay rise and improved conditions, with members now considering a 2.75 per cent increase as part of a package including free bus travel for and a one-off $1000 payment.
RTBU NSW secretary Alex Claassens said progress had been made after marathon 10-hour negotiations on Monday which spilled over to Tuesday but he stopped short of saying the deal was a good one.
