You can use mtext()

par(mar=c(5.1,4.1,4.1,5.1))
plot(x$Time, x$y1, type='l', bty = 'c', col = 'red')
par(new = TRUE)
plot(x$Time, x$y2, type = 'l', axes = FALSE, xlab = '', ylab = '', col=
'green')
axis(4, col='green')
mtext(side=4, text="label green", line=2)
par(new = TRUE)
plot(x$Time, x$y3, type = 'l', axes = FALSE, xlab = '', ylab = '', col =
'blue')
axis(4, col='blue', line = -4)
mtext(side=4, text="label green", line=-2)

Walmes.

==========================================================================
Walmes Marques Zeviani
LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
Departamento de Estatística - Universidade Federal do Paraná
fone: (+55) 41 3361 3573
VoIP: (3361 3600) 1053 1173
e-mail: walmes@ufpr.br
twitter: @walmeszeviani
homepage: http://www.leg.ufpr.br/~walmes
linux user number: 531218
==========================================================================

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