It appears that you are retained as Worker or a Self-Employed Independent Contractor via an Agency with the Government as opposed to having the status of a full-time permanent Employee. Therefore, your scope to object to the changes to your fees and payment terms is limited to breach of contract for unilateral variations to the contract when you have not provided consent.
Variations to employment contracts (as with all commercial contracts) must be agreed by both parties to be effective. You may expressly consent to the variation of your employment contract and perform your new role as your employer requires.
Otherwise, you may refuse the change and if your employer terminates the contract or you are forced to terminate it as a direct result of the change, you may claim breach of contract in the civil County Courts or the Regional Employment Tribunals.
If you believe that the employer attempted to vary your contract from its original terms without your consent, this is a potential breach of contract entitling you to terminate the contract and claim damages.
If you are unhappy with the new terms of the contract, I strongly recommend that you object as soon as possible by setting out your reasons in writing. If the parties are unable to reach an amicable resolution to the dispute, you should terminate the contract and present a letter of claim for breach of contract before issuing court or tribunal proceedings against the employer.
If you delay for too long before objecting to the change and terminating in response, the court or tribunal may consider that you have affirmed the variation by conduct and waived any potential rights you may have had under breach of contract.