Configuring FPGA through EPCS (EEPROM) INCLUDING Nios II program?

That is the EPCS flash loader sequence.

What you should be able to do is extrace the sections from the elf file and use each one to generate an initialisation file for the relevant memory block.

I generate an elf file that includes two code and two data sections that need initialising (and some sections that don't).

$ objdump -h mtp2.elf
mtp2.elf:     file format elf32-little
Sections:
Idx Name          Size      VMA       LMA       File off  Algn
  0 prot_code     00002078  00008000  00008000  000000f4  2**2
                  CONTENTS, ALLOC, LOAD, READONLY, CODE
  1 hdlc_code     00000a50  0000c000  0000c000  0000216c  2**2
                  CONTENTS, ALLOC, LOAD, READONLY, CODE
  2 shared_data   00002000  00014000  00014000  00002bbc  2**2
                  ALLOC
  3 prot_data     00002b3c  00018000  00018000  00002bbc  2**4
                  CONTENTS, ALLOC, LOAD, DATA
  4 hdlc_data     00002e08  0001c000  0001c000  000056f8  2**2
                  CONTENTS, ALLOC, LOAD, DATA
  5 sdram         00a38000  01000000  01000000  00008500  2**15
                  ALLOC
  6 .comment      000001ce  00000000  00000000  00008500  2**0
                  CONTENTS, READONLY
  7 unwanted      00000000  0001c000  0001c000  000056f8  2**0
                  CONTENTS, ALLOC, LOAD, CODE

I actually use objcopy to convert them into ppc object files, but I generate raw binary files on the way.

Makefile fragment below:

# Convert sections from nios2 program into readonly data areas that can
#  be linked into the loading program.
#  We must cd to $(OBJDIR) to avoid getting the directory path prepended
#  to the symbol names objcopy adds to the created file.
#  Flags for objcopy to generate the correct section type from raw data
SECT = $(notdir $(@:.o=))
FL_GEN = --rename-section .data=.rodata.$(SECT),alloc,load,readonly,data,contents
OBJ_FLAGS = -O elf32-powerpc -B powerpc
$(NIOS_SECT_OBJS): $(OBJ_DIR)/mtp2.elf
        @ echo '### create $@'
        $(NIOS_OBJCOPY) -O binary -j $(SECT) $^ $(@:.o=.x)
        cd $(OBJ_DIR) && { 
              $(OBJCOPY) -I binary $(OBJ_FLAGS) $$FL_GEN $(SECT:=.x) $(SECT:=.o); 
        }
        rm -f $(@:.o=.x)

I'm not sure what format you need the M9K initialisation data in, you might not need two objcopy call, and you'll certainly need different values for OBJ_FLAGS for the second one.