Firstly, the sentence contains reported speech, which is the part set in quotes: it indicates that those were the exact words used by the agency.
However, this reported speech is not a quote in the sense that it is grammatically integrated into the sentence, which makes perfect sense if the quotes are removed. The only meaning which is lost is the indication "these were the exact words used".
So let us drop the quotes:
The agency said that the procedure it set back in the 1970s for revising rules for older drugs was not rapid, but there were many fewer steps to the process that today is long.
This sentence reports what the agency said. The major structure is:
The agency said that [clause ...].
The clause is:
The procedure it set back in the 1970s for revising rules for older drugs was not rapid, but there were many fewer steps to the process that today is long.
The clause is actually two clauses, connected by the conjuction "but". The major features are:
The procedure [ ... ] was not rapid, but there were fewer steps [ ... ].
They are saying that although the old procedure procedure was not fast, but it was faster than it is today because it had fewer steps.
- The agency established a procedure in the 1970's.
- The established procedure is for revising rules.
- The rules that are revised are rules which apply to older drugs (perhaps regulating producing the drugs, transporting them, packating, labeling, storing, prescribing, administering, et cetera: we don't know these details from the sentence).
- The procedure for revising these rules was not rapid.
- Although the procedure was not rapid, it still had fewer steps compared to today's process.
- Today's procedure for revising the rules is long.
- "There were many steps to the process" means that the had many steps. This is a usage of "to" which is very similar to: "there is nothing to it, it is easy!"
- "There were many fewer steps to the process" means that the process had fewer steps (compared to some other process, like the one used today), and the difference was many. For instance: "I have many fewer cookies than you" means exactly the same thing as "you have many more cookies than me": I would need to have many more cookies in order to match how many you have. Thus, the, slow, old process would have to have many more steps added to it to match the even longer, slower new process.
- "Process that today is long" might be clearer if it is written "Process that, today, is long". It is a rearrangement of "process that is long today", which emphasizes "today" by moving it to the left, denoting a process which wasn't long before, but has become long.
In other words, the agency essentially said, "We're not saying that the old 1970's procedures for revising old drug rules were fast --- they weren't, by any means --- but the modern ones have many more steps and take even longer".