Presumably this is binary? At least the remark about $2^m-1$ points that way.
Anyway, over a field of characteristic two cyclotomic cosets modulo $n$ are the sets of the form $C(j,n)=\{k\in\Bbb{Z}_{n}\mid k\equiv 2^i j\pmod{n}\ \text{for some natural number $i$}\}$. So when $n=45$ we get
$$
\begin{aligned}
C(0,45)&=\{0\}\\
C(1,45)&=\{1,2,4,8,16,32,19,38,31,17,34,23\}\\
C(3,45)&=\{3,6,12,24\}\\
C(5,45)&=\{5,10,20,40,35,25\}\\
C(7,45)&=\{7,14,28,11,22,44,43,41,37,29,13,26\}=-C(1)\\
C(9,45)&=\{9,18,36,27\}\\
C(15,45)&=\{15,30\}\\
C(21,45)&=\{21,42,39,33\}=-C(3)
\end{aligned}
$$
So you see that the minimal polynomial of a root of unity $\zeta$ of order $45$ is of degree twelve. The cyclotomic polynomial (over $\Bbb{Q}$)
$$
\Phi_{45}(x)=\frac{(x^{45}-1)(x^3-1)}{(x^{15}-1)(x^9-1)}=x^{24}-x^{21}+x^{15}-x^{12}+x^9-x^3+1.
$$
is of degree 24, so it splits into a product of two irreducible factors - both of degree 12. The zeros of these two factors are $\zeta^k$ with $k\in C(1,45)$ and $k\in C(7,45)$ respectively. As $C(7,45)\equiv-C(1,45)\pmod{45}$, the two factors will be reciprocals of each other. I guess we could take advantage of this bit in figuring them out. But it is more efficient to take advantage of the fact that $\zeta^3$ is of order fifteen. Because 15 is still divisible by three, we also get the converse. If $\omega$ is of order fifteen, and $\alpha^3=\omega$, then $\alpha$ will necessarily be of order $45$. As $15$ is of the form $2^m-1$ for $m=4$ we can utilize the factorization of $\Phi_{15}(x)$ over the binary field. Even Matlab should be able to give you that. I happen to have it memorized, so let's just state that
$$
\Phi_{15}(x)=x^8-x^7+x^5-x^4+x^3-x+1\equiv(x^4+x+1)(x^4+x^3+1)\pmod 2.
$$
Let the two factors here be $f_1(x)=x^4+x+1$ and $f_2(x)=x^4+x^3+1$.
In view of the above the factors of $\Phi_{45}(x)$ in $\Bbb{F}_2[x]$ must be
$$
f_1(x^3)=x^{12}+x^3+1\qquad\text{and}\qquad f_2(x^3)=x^{12}+x^9+1.
$$