The cipher's used by Control-M MFT and AFT can be customized by modifying the <agent home>/ctm_agent/ctm/cm/AFT/data/aft_configurable.properties file.
The ciphers are controlled by 2 lines that list the ciphers currently supported.
To remove a cipher delete it from the list.
Make sure the list starts with a cipher, and is comma delimited with no spaces.
The ciphers are tried in the order they are listed.

NOTE: Each parameter is only 1 line.  before making any changes back up your existing configuration file.

Default Settings for AFT 8.2.X and MFT 9.X
SFTP:
com.bmc.aft.configurable.sftp.All.Ciphers=aes128-cbc,aes192-cbc,aes256-cbc,aes128-ctr,aes192-ctr,aes256-ctr,3des-cbc,3des-ctr,blowfish-cbc,arcfour256,arcfour128,arcfour

FTP Over SSL:
com.bmc.aft.configurable.fts.ftp.All.Ciphers=TLS_ECDHE_ECDSA_WITH_AES_128_CBC_SHA256,TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA256,TLS_RSA_WITH_AES_128_CBC_SHA256,TLS_ECDH_ECDSA_WITH_AES_128_CBC_SHA256,TLS_ECDH_RSA_WITH_AES_128_CBC_SHA256,TLS_DHE_RSA_WITH_AES_128_CBC_SHA256,TLS_DHE_DSS_WITH_AES_128_CBC_SHA256,TLS_ECDHE_ECDSA_WITH_AES_128_CBC_SHA,TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA,TLS_RSA_WITH_AES_128_CBC_SHA,TLS_ECDH_ECDSA_WITH_AES_128_CBC_SHA,TLS_ECDH_RSA_WITH_AES_128_CBC_SHA,TLS_DHE_RSA_WITH_AES_128_CBC_SHA,TLS_DHE_DSS_WITH_AES_128_CBC_SHA,TLS_ECDHE_ECDSA_WITH_AES_128_GCM_SHA256,TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256,TLS_RSA_WITH_AES_128_GCM_SHA256,TLS_ECDH_ECDSA_WITH_AES_128_GCM_SHA256,TLS_ECDH_RSA_WITH_AES_128_GCM_SHA256,TLS_DHE_RSA_WITH_AES_128_GCM_SHA256,TLS_DHE_DSS_WITH_AES_128_GCM_SHA256,TLS_ECDHE_ECDSA_WITH_3DES_EDE_CBC_SHA,TLS_ECDHE_RSA_WITH_3DES_EDE_CBC_SHA,SSL_RSA_WITH_3DES_EDE_CBC_SHA,TLS_ECDH_ECDSA_WITH_3DES_EDE_CBC_SHA,TLS_ECDH_RSA_WITH_3DES_EDE_CBC_SHA,SSL_DHE_RSA_WITH_3DES_EDE_CBC_SHA,SSL_DHE_DSS_WITH_3DES_EDE_CBC_SHA,TLS_ECDHE_ECDSA_WITH_RC4_128_SHA,TLS_ECDHE_RSA_WITH_RC4_128_SHA,SSL_RSA_WITH_RC4_128_SHA,TLS_ECDH_ECDSA_WITH_RC4_128_SHA,TLS_ECDH_RSA_WITH_RC4_128_SHA,SSL_RSA_WITH_RC4_128_MD5,TLS_EMPTY_RENEGOTIATION_INFO_SCSV,TLS_DH_anon_WITH_AES_128_GCM_SHA256,TLS_DH_anon_WITH_AES_128_CBC_SHA256,TLS_ECDH_anon_WITH_AES_128_CBC_SHA,TLS_DH_anon_WITH_AES_128_CBC_SHA,TLS_ECDH_anon_WITH_3DES_EDE_CBC_SHA,SSL_DH_anon_WITH_3DES_EDE_CBC_SHA,TLS_ECDH_anon_WITH_RC4_128_SHA,SSL_DH_anon_WITH_RC4_128_MD5,SSL_RSA_WITH_DES_CBC_SHA,SSL_DHE_RSA_WITH_DES_CBC_SHA,SSL_DHE_DSS_WITH_DES_CBC_SHA,SSL_DH_anon_WITH_DES_CBC_SHA,SSL_RSA_EXPORT_WITH_DES40_CBC_SHA,SSL_DHE_RSA_EXPORT_WITH_DES40_CBC_SHA,SSL_DHE_DSS_EXPORT_WITH_DES40_CBC_SHA,SSL_DH_anon_EXPORT_WITH_DES40_CBC_SHA,SSL_RSA_EXPORT_WITH_RC4_40_MD5,SSL_DH_anon_EXPORT_WITH_RC4_40_MD5,TLS_RSA_WITH_NULL_SHA256,TLS_ECDHE_ECDSA_WITH_NULL_SHA,TLS_ECDHE_RSA_WITH_NULL_SHA,SSL_RSA_WITH_NULL_SHA,TLS_ECDH_ECDSA_WITH_NULL_SHA,TLS_ECDH_RSA_WITH_NULL_SHA,TLS_ECDH_anon_WITH_NULL_SHA,SSL_RSA_WITH_NULL_MD5,TLS_KRB5_WITH_3DES_EDE_CBC_SHA,TLS_KRB5_WITH_3DES_EDE_CBC_MD5,TLS_KRB5_WITH_RC4_128_SHA,TLS_KRB5_WITH_RC4_128_MD5,TLS_KRB5_WITH_DES_CBC_SHA,TLS_KRB5_WITH_DES_CBC_MD5,TLS_KRB5_EXPORT_WITH_DES_CBC_40_SHA,TLS_KRB5_EXPORT_WITH_DES_CBC_40_MD5,TLS_KRB5_EXPORT_WITH_RC4_40_SHA,TLS_KRB5_EXPORT_WITH_RC4_40_MD5


1. Navigate to <agent home>/cm/AFT/data
2. Make a backup copy of aft_configurable.properties
3. Edit aft_configurable.properties and modify the parameters as needed:
    a.  For SSL adjust the parameter:  com.bmc.aft.configurable.fts.ftp.All.Ciphers
    b.  For SFTP adjust the paramater:  com.bmc.aft.configurable.sftp.All.Ciphers
4.  Logon as the Agent user where MFT is installed for UNIX/LINUX ; For Windows open a cmd prompt as administrator.

NOTE: The following step will cause currently running file transfer jobs to terminate and fail.

5.  Recycle the MFT/AFT container by navigating to <agent home>/ctm/cm/AFT/exe and running the commands:
      ctmaftcontainer stop 
      ctmaftcontainer start

================================
Starting with MFT 9.0.20, Ciphers (sftp.ciphers), KEX Algorithms (sftp.kex), and MAC (sftp.mac) for SFTP Connections can be specified at the Connection Profile's "Additional Settings" as documented
Control-M 9.0.20.200 Control-M Documentation - Control-M - BMC Documentation

For example: