This question is 2 year old, but I managed to solved it.
First you must enable xterm-keys in your tmux config. So put the following in ~/.tmux.conf
setw -g xterm-keys on
But, this will break other key combinations. To fix them, put the following in your ~/.emacs or ~/.emacs.d/init.el config
;; handle tmux's xterm-keys
;; put the following line in your ~/.tmux.conf:
;; setw -g xterm-keys on
(if (getenv "TMUX")
(progn
(let ((x 2) (tkey ""))
(while (<= x 8)
;; shift
(if (= x 2)
(setq tkey "S-"))
;; alt
(if (= x 3)
(setq tkey "M-"))
;; alt + shift
(if (= x 4)
(setq tkey "M-S-"))
;; ctrl
(if (= x 5)
(setq tkey "C-"))
;; ctrl + shift
(if (= x 6)
(setq tkey "C-S-"))
;; ctrl + alt
(if (= x 7)
(setq tkey "C-M-"))
;; ctrl + alt + shift
(if (= x 8)
(setq tkey "C-M-S-"))
;; arrows
(define-key key-translation-map (kbd (format "M-[ 1 ; %d A" x)) (kbd (format "%s<up>" tkey)))
(define-key key-translation-map (kbd (format "M-[ 1 ; %d B" x)) (kbd (format "%s<down>" tkey)))
(define-key key-translation-map (kbd (format "M-[ 1 ; %d C" x)) (kbd (format "%s<right>" tkey)))
(define-key key-translation-map (kbd (format "M-[ 1 ; %d D" x)) (kbd (format "%s<left>" tkey)))
;; home
(define-key key-translation-map (kbd (format "M-[ 1 ; %d H" x)) (kbd (format "%s<home>" tkey)))
;; end
(define-key key-translation-map (kbd (format "M-[ 1 ; %d F" x)) (kbd (format "%s<end>" tkey)))
;; page up
(define-key key-translation-map (kbd (format "M-[ 5 ; %d ~" x)) (kbd (format "%s<prior>" tkey)))
;; page down
(define-key key-translation-map (kbd (format "M-[ 6 ; %d ~" x)) (kbd (format "%s<next>" tkey)))
;; insert
(define-key key-translation-map (kbd (format "M-[ 2 ; %d ~" x)) (kbd (format "%s<delete>" tkey)))
;; delete
(define-key key-translation-map (kbd (format "M-[ 3 ; %d ~" x)) (kbd (format "%s<delete>" tkey)))
;; f1
(define-key key-translation-map (kbd (format "M-[ 1 ; %d P" x)) (kbd (format "%s<f1>" tkey)))
;; f2
(define-key key-translation-map (kbd (format "M-[ 1 ; %d Q" x)) (kbd (format "%s<f2>" tkey)))
;; f3
(define-key key-translation-map (kbd (format "M-[ 1 ; %d R" x)) (kbd (format "%s<f3>" tkey)))
;; f4
(define-key key-translation-map (kbd (format "M-[ 1 ; %d S" x)) (kbd (format "%s<f4>" tkey)))
;; f5
(define-key key-translation-map (kbd (format "M-[ 15 ; %d ~" x)) (kbd (format "%s<f5>" tkey)))
;; f6
(define-key key-translation-map (kbd (format "M-[ 17 ; %d ~" x)) (kbd (format "%s<f6>" tkey)))
;; f7
(define-key key-translation-map (kbd (format "M-[ 18 ; %d ~" x)) (kbd (format "%s<f7>" tkey)))
;; f8
(define-key key-translation-map (kbd (format "M-[ 19 ; %d ~" x)) (kbd (format "%s<f8>" tkey)))
;; f9
(define-key key-translation-map (kbd (format "M-[ 20 ; %d ~" x)) (kbd (format "%s<f9>" tkey)))
;; f10
(define-key key-translation-map (kbd (format "M-[ 21 ; %d ~" x)) (kbd (format "%s<f10>" tkey)))
;; f11
(define-key key-translation-map (kbd (format "M-[ 23 ; %d ~" x)) (kbd (format "%s<f11>" tkey)))
;; f12
(define-key key-translation-map (kbd (format "M-[ 24 ; %d ~" x)) (kbd (format "%s<f12>" tkey)))
;; f13
(define-key key-translation-map (kbd (format "M-[ 25 ; %d ~" x)) (kbd (format "%s<f13>" tkey)))
;; f14
(define-key key-translation-map (kbd (format "M-[ 26 ; %d ~" x)) (kbd (format "%s<f14>" tkey)))
;; f15
(define-key key-translation-map (kbd (format "M-[ 28 ; %d ~" x)) (kbd (format "%s<f15>" tkey)))
;; f16
(define-key key-translation-map (kbd (format "M-[ 29 ; %d ~" x)) (kbd (format "%s<f16>" tkey)))
;; f17
(define-key key-translation-map (kbd (format "M-[ 31 ; %d ~" x)) (kbd (format "%s<f17>" tkey)))
;; f18
(define-key key-translation-map (kbd (format "M-[ 32 ; %d ~" x)) (kbd (format "%s<f18>" tkey)))
;; f19
(define-key key-translation-map (kbd (format "M-[ 33 ; %d ~" x)) (kbd (format "%s<f19>" tkey)))
;; f20
(define-key key-translation-map (kbd (format "M-[ 34 ; %d ~" x)) (kbd (format "%s<f20>" tkey)))
(setq x (+ x 1))
))
)
Also I have my solution in archlinux wiki