The manual man mkfs.fat suggests the option -S

-S LOGICAL-SECTOR-SIZE Specify the number of bytes per logical sector. Must be a power of 2 and greater than or equal to 512, i.e. 512, 1024, 2048, 4096, 8192, 16384, or 32768.

Before running the command, please double-check, that you will format the correct partition, and not a partition with valuable data.

I hope this will work for you,

if connected via USB sudo mkfs.fat -S 4096 /dev/sdxn where x is the drive letter and n is the partition number, or

if connected via PCI sudo mkfs.fat -S 4096 /dev/mmcblkmpn where m is the device number (probably 0) and n is the partition number.

You will find how the card is connected via the following commands

sudo lsblk -f sudo lsblk -m sudo parted -ls

Check the sector size with for example

sudo fsck.fat -v /dev/sdxn

Some other tools may not show the sector size of the FAT file system. The important thing is that it will work for your application.

Example: I had the following result