From looking at the documentation, it looks like the correct way to do this is with the "submit_parameter" function. For example (untested):

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
$factory->submit_parameter('word_size', 11);
my $r = $factory->submit_blast($input);

Available parameters, from the source, are:

our %PUTPARAMS = (
'AUTO_FORMAT'       => '(Off|(Semi|Full)auto)',     # Off, Semiauto, Fullauto
'COMPOSITION_BASED_STATISTICS'      => '(0|1)',     # yes, no on NCBI's site, but actually binary 0/1
'DATABASE'  =>  '.*',
'DB_GENETIC_CODE' => '([1-9]|1[1-6]|2(1|2))',   # 1..16,21,22
'DISPLAY_SORT'   => '\d',
'ENDPOINTS' => '(yes|no)',                  # yes,no
'ENTREZ_QUERY'      => '.*',
'EXPECT'    => '\d+(\.\d+)?([eE]-\d+)?',    # Positive double
'FILTER'    => '[LRm]',                     # L or R or m
'GAPCOSTS'  => '-?\d+(\.\d+)\s+-?\d+(\.\d+)',
                                # Two space separated float values
'GENETIC_CODE'      => '([1-9]|1[1-6]|2(1|2))',     # 1..16,21,22
'HITLIST_SIZE'      => '\d+',                       # Positive integer
'I_THRESH'  => '-?\d+(\.\d+)([eE]-\d+)?',   # float
'LAYOUT'    => '(One|Two)Windows?',         # onewindow, twowindows
'LCASE_MASK'        => '(yes|no)',                  # yes, no
'MATRIX_NAME'       => '.*',
'NUCL_PENALTY'      => '-\d+',                      # Negative integer
'NUCL_REWARD'       => '-?\d+',                     # Integer
'OTHER_ADVANCED' => '.*',
'PERC_IDENT'        => '\d\d+',                     # Integer, 0-99 inclusive
'PHI_PATTERN'       => '.*',
'PROGRAM'   => 't?blast[pnx]',
                                # tblastp, tblastn, tblastx, blastp, blastn, blastx
'QUERY'             => '.*',
'QUERY_FILE'        => '.*',
'QUERY_BELIEVE_DEFLINE'     => '(yes|no)',          # yes, no
'QUERY_FROM'        => '\d+',                       # Positive integer
'QUERY_TO'  => '\d+',                       # Positive integer
'SEARCHSP_EFF'      => '\d+',                       # Positive integer
'SERVICE'   => '(plain|p[sh]i|(rps|mega)blast)',
                                # plain,psi,phi,rpsblast,megablast
'SHORT_QUERY_ADJUST' => '(true|false)',
'THRESHOLD' => '-?\d+',                     # Integer
'UNGAPPED_ALIGNMENT' => '(yes|no)',         # yes, no
'WORD_SIZE' => '\d+'                        # Positive integer
                                  );

Thanks Niek for reply.

I don't manage to find how to change the parameters for gap opening/extension and mismatch penality.

my $prog = 'blastn';
my $db   = 'nr';
my $e_val= '1e-10';
my $v = 1;

my @params = (
    '-prog' => $prog,
    '-data' => $db,
    '-expect' => $e_val,
    '-readmethod' => 'SearchIO');

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
my $seq_blast = Bio::SeqIO ->new (-file =>$fasta_interet, -format =>'fasta');

while (my $input = $seq_blast -> next_seq()){
    my $r = $factory->submit_blast($input);
    print STDERR "waiting..." if( $v > 0 );
    while ( my @rids = $factory->each_rid ) {
        foreach my $rid ( @rids ) {
            my $rc = $factory->retrieve_blast($rid);
            if( !ref($rc) ) {
                if( $rc < 0 ) {
                    $factory->remove_rid($rid);
                }
                print STDERR "." if ( $v > 0 );
                sleep 5;
            } 
            else {
                my $result = $rc->next_result();                    
                my $filename = "out_remote.blast";
                $factory->save_output($filename);
                $factory->remove_rid($rid);
            }
        }
    }
}