The body which represents train firms and Network Rail had described the proposals as their "best and final".
RMT boss Mick Lynch branded the offers "dreadful", while the transport secretary called the move "a kick in the teeth for passengers".
The rejection was made by the national executive committee but the industry and government want a members' vote.
Twenty officials and representatives sit on the body but the RMT said the decision was made following a wide-ranging consultation with every level of the union involved in the national rail dispute.
Mr Lynch said the offers did not meet members' expectations "on pay, job security or working conditions".
The RMT said it would now seek further meetings with Network Rail and the Rail Delivery Group (RDG) - which represents train operating companies - to try to work towards a settlement.
But it will start preparing to re-ballot its members when the existing strike mandate runs out in late May.
It is a significant moment in the ongoing national rail dispute - not just because the RMT has rejected what were billed as final offers from the employers, but because the union is now talking explicitly about seeking an "unconditional" pay deal.
The government and industry have said all along that a pay increase would have to be funded by "reforms".
There had been movement in the dispute in recent months and on all sides the tone had become less antagonistic. But it is clearly not as close to a resolution as some onlookers had hoped.
The RDG said on Friday that passengers and "many hard-working RMT members will be deeply dismayed that the union leadership has opted to reject our fair proposals without putting out a vote to their full membership in a democratic referendum".
It said it had made "substantial changes" to its offer after recent negotiations, including a minimum 9% pay increase over two years which rail workers "will now miss out on, without even having had an opportunity to have their say".
"We removed driver-only operation and gave an improved job security offer," the group said, adding: "The railway's financial crisis is not going away."
"The RMT leadership must now accept the urgent need to make the railway fit for the future for both our people, and the communities the railway serves," it said.
Last month, the RDG put forward a list of changes to working practices which it said could fund a 5% pay rise for 2022 and a further 4% this year.
Separately Network Rail, whose employees include maintenance and signalling staff, offered a package including a 5% pay increase last year and 4% for 2023, plus other benefits such as discounted travel for family. Members rejected this in December.
Network Rail recently put forward a slightly updated offer, but kept the pay element the same.
The RMT said it was seeking "an unconditional pay offer, a job security agreement and no detrimental changes being imposed on members terms, conditions and working practices".
The transport secretary echoed the rail industry's position that RMT members should be given a vote on the deals on the table.
Mark Harper said workers are "being blocked from having a say on their own future" and that a decision had been made for them behind closed doors.
Planned changes to how maintenance teams at Network Rail work are a particular point of contention for the RMT.
The union said it viewed proposed plans as "unsafe" and unworkable. Network Rail has always insisted safety would not be compromised.
Mr Lynch said: "We have carried out an in-depth consultation of our 40,000 members and the message we have received, loud and clear, is to reject these dreadful offers.
"Our members cannot accept the ripping up of their terms and conditions or to have safety standards on the railway put into jeopardy under the guise of so-called modernisation.
"If our union did accept these offers, we would see a severe reduction in scheduled maintenance tasks, making the railways less safe, the closure of all ticket offices, and thousands of jobs stripped out of the industry when the railways need more investment, not less."
Network Rail's chief negotiator Tim Shovellor claimed employees want to accept the offer and said the RMT "refuses to listen and instead takes soundings from the echo chamber of its most active members."
This is separate to the train drivers' dispute. The drivers' main union, Aslef, says it hopes to have more talks next week.
A smaller union, the TSSA, said on Friday that thousands of its members would be given a vote on the offers from the train companies.