To begin with, I assume that this is the normal Macintosh SE (with an 800K floppy drive), not the FDHD variant.
The diskettes in this case must be 2DD (DSDD), not HD. The magnetic material is not the same. HD floppies have an HD mark and an extra (square) hole.
As a very temporary workaround, if no 2DD (DSDD) diskettes are available, one can cover the extra hole in an HD floppy with a piece of tape (in order to make it appear like a DD disk to floppy drives that can recognise/handle both types). However, this is not a stable solution (and may not always work), and it is not recommended.
An existing 2DD diskette can be erased/reformatted to the 800K Mac format in the Macintosh SE.
Look for a "System Folder" on the hard disk. If that folder is smaller than 800K, try to drag (copy) it to an empty 800K floppy. That should provide you with a basic startup floppy.
Can any disk utility be seen on the hard disk?
If you somehow could gain access to an approx. 1992-1997 Macintosh computer, it would be possible to create a set of System 6.0.8 (800K) floppies. Disk test and formatting utilities are included.
http://download.info.apple.com/Apple_Support_Area/Apple_Software_Updates/English -North_American/Macintosh/System/Older_System/System_6.0.x/SSW_6.0.8-800k_Disk1o f4.sea.bin
http://download.info.apple.com/Apple_Support_Area/Apple_Software_Updates/English -North_American/Macintosh/System/Older_System/System_6.0.x/SSW_6.0.8-800k_Disk2o f4.sea.bin
http://download.info.apple.com/Apple_Support_Area/Apple_Software_Updates/English -North_American/Macintosh/System/Older_System/System_6.0.x/SSW_6.0.8-800k_Disk3o f4.sea.bin
http://download.info.apple.com/Apple_Support_Area/Apple_Software_Updates/English -North_American/Macintosh/System/Older_System/System_6.0.x/SSW_6.0.8-800k_Disk4o f4.sea.bin
One would need an appropriate version of StuffIt Expander (such as 4.0.1 or 5.5) for the .bin (MacBinary) decoding. Furthermore, Disk Copy 4.2 (the Make A Copy button) is used to create floppies from the disk images.
http://download.info.apple.com/Apple_Support_Area/Apple_Software_Updates/English -North_American/Macintosh/Utilities/Disk_Copy/Disk_Copy_4.2.sea.bin