There are 3 ways to reduce EMI.
First one is adding shielding materials.
Advantage:
It will seal the radiation inside your system.
Disadvantage:
high cost.
Second one is to use spread spectrum oscillator.
Advantage:
lower down the EMI with low extra cost.
Disadvantage:
Using spread spectrum means adding jitter. It is going to increase your system bit error rate. It may cause the system failure.
We have this kind of experience with one of our customer.
The third one is using high frequency & high performance crystal oscillator or ICs.
Advantage:
This kind of products are low noise inside, so they can run into high frequency & usually generate much less radiation. All of our products are designed with extremely low noise & high frequency. The EMI radiation is from the sum of all the ICs inside your system. By carefully choosing driver ICs such as crystal oscillator, clock buffer, TTL logic etc. can reduce the total EMI radiation from your system.
Disadvantage:
If the high radiation is from the main chip that you are not able to change, you will not be able to fix your EMI problem.